Contacts of the helix formed by residues 311 - 336 (chain C) in PDB entry 1UMD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 311 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG* 5.9 1.8 - - - +
310C TRP* 1.3 95.8 - - - +
312C GLU* 1.3 62.9 + - - +
313C GLU* 3.2 13.4 + - - +
314C TRP* 2.7 47.7 + - - +
315C GLU 3.1 9.2 + - - -
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Residues in contact with GLU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C TRP* 3.6 22.6 - - + -
311C ASN* 1.3 72.1 - - - +
313C GLU* 1.3 67.3 + - - +
315C GLU* 3.2 7.4 + - + +
316C GLU* 2.4 57.9 + - - +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ASN* 3.2 11.9 + - - +
312C GLU* 1.3 86.4 + - - +
314C TRP* 1.3 64.2 + - - +
316C GLU* 3.3 8.8 + - + +
317C ASP* 3.0 41.2 + - - +
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Residues in contact with TRP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 2.9 79.8 - - + +
42C TYR* 3.5 29.4 - + - -
43C ARG* 4.8 7.9 - - + -
304C LEU* 4.2 3.8 - - + -
309C LEU 3.8 13.5 - - - -
310C TRP* 3.6 22.7 - + - -
311C ASN* 2.7 28.2 + - - +
313C GLU* 1.3 70.8 - - - +
315C GLU* 1.3 65.8 + - - +
317C ASP* 3.2 11.4 + - + -
318C VAL* 2.8 54.3 + - + +
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 2.7 31.0 + - - -
46C LEU* 3.9 7.0 - - - +
301C ARG* 3.8 5.0 + - - -
310C TRP* 2.8 33.2 + - + +
311C ASN 3.1 4.9 + - - -
312C GLU* 3.2 14.1 - - + +
314C TRP* 1.3 79.1 - - - +
316C GLU* 1.3 62.5 + - + +
318C VAL* 3.8 4.6 - - - +
319C ARG* 2.6 72.6 + - - +
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 2.4 43.1 + - - +
313C GLU* 3.4 11.8 - - + +
314C TRP 3.2 0.2 - - - -
315C GLU* 1.3 81.3 - - + +
317C ASP* 1.3 67.0 + - - +
319C ARG* 3.4 4.6 + - - +
320C GLU* 3.0 45.2 + - - +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLU* 3.0 34.2 + - - +
314C TRP* 3.8 12.6 - - + +
316C GLU* 1.3 80.2 - - - +
318C VAL* 1.3 58.0 + - - +
320C GLU* 3.5 13.0 + - - +
321C GLU* 2.9 46.0 + - - +
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 6.1 0.2 - - + -
43C ARG* 3.8 26.0 - - + +
46C LEU* 3.8 18.8 - - + -
314C TRP* 2.8 62.5 + - + +
315C GLU* 3.8 3.4 - - - +
317C ASP* 1.3 73.4 - - + +
319C ARG* 1.3 59.3 + - - +
321C GLU* 3.2 12.6 + - - +
322C ILE* 2.9 46.4 + - + +
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Residues in contact with ARG 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.5 26.8 - - + +
49C ARG* 5.9 4.2 - - - +
50C MET* 3.4 45.9 - - + +
53C GLU* 5.0 5.3 + - - -
297C ILE* 5.0 6.1 - - - +
315C GLU* 2.6 52.6 + - - +
316C GLU* 3.9 4.5 - - - +
318C VAL* 1.3 77.1 - - - +
320C GLU* 1.3 58.2 + - + +
322C ILE* 3.3 0.6 + - - -
323C ARG* 2.9 26.8 + - - +
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C GLU* 3.0 39.1 + - - +
317C ASP* 3.8 12.6 - - - +
319C ARG* 1.3 79.1 - - + +
321C GLU* 1.3 61.2 + - - +
323C ARG* 3.4 33.3 + - - +
324C ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.3 24.5 + - - +
314C TRP* 6.2 0.2 - - - -
317C ASP* 2.9 38.3 + - - +
318C VAL* 3.5 10.0 + - - +
320C GLU* 1.3 77.5 - - + +
322C ILE* 1.3 58.1 + - - +
324C ALA* 3.3 8.2 + - - +
325C GLU* 3.0 32.8 + - - +
328C ARG* 5.2 0.2 + - - -
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Residues in contact with ILE 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.9 23.3 - - - +
46C LEU* 3.8 17.3 - - + +
47C ALA* 3.4 39.9 - - + +
50C MET* 3.8 31.2 - - + -
108C LEU* 6.5 0.2 - - + -
318C VAL* 2.9 30.4 + - + +
319C ARG* 3.7 4.5 - - - +
321C GLU* 1.3 73.9 - - - +
323C ARG* 1.3 66.0 + - - +
325C GLU* 3.0 12.9 + - - +
326C LEU* 2.9 31.5 + - + +
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Residues in contact with ARG 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C MET* 4.1 14.1 - - + -
54C ARG* 4.3 15.0 - - - +
319C ARG 2.9 16.9 + - - +
320C GLU* 3.6 33.2 + - - +
321C GLU 3.3 0.2 - - - -
322C ILE* 1.3 76.2 - - - +
324C ALA* 1.3 58.3 + - - +
326C LEU* 3.3 8.8 + - - +
327C GLU* 3.0 36.1 + - + +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C GLU 3.1 14.1 + - - +
321C GLU* 3.5 10.5 - - - +
323C ARG* 1.3 76.6 - - - +
325C GLU* 1.3 63.2 + - - +
327C GLU* 3.4 9.0 + - - +
328C ARG* 3.0 37.9 + - - +
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Residues in contact with GLU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 2.8 44.8 + - - -
47C ALA* 5.5 1.4 - - - +
108C LEU* 3.5 22.7 - - + +
321C GLU* 3.0 16.2 + - - +
322C ILE* 3.0 15.0 + - - +
324C ALA* 1.3 77.4 - - - +
326C LEU* 1.3 56.4 + - - +
328C ARG* 3.4 28.6 + - - +
329C GLY 2.8 24.8 + - - -
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA 5.5 0.4 - - - +
50C MET* 3.7 31.9 - - + +
51C LEU* 3.9 22.2 - - + +
54C ARG* 4.1 32.4 - - + +
102C LEU* 5.9 1.1 - - + -
108C LEU* 3.8 30.5 - - + -
112C LEU* 4.2 5.2 - - + +
322C ILE* 2.9 31.4 + - + +
323C ARG* 3.3 12.5 + - - +
325C GLU* 1.3 77.4 - - - +
327C GLU* 1.3 56.6 + - - +
329C GLY* 3.3 0.5 + - - -
330C LEU* 2.9 33.3 + - - +
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 2.6 38.9 + - - +
323C ARG* 3.0 28.8 + - + +
324C ALA* 3.6 8.3 - - - +
325C GLU 3.3 0.2 - - - -
326C LEU* 1.3 77.8 - - - +
328C ARG* 1.3 57.7 + - - +
330C LEU* 3.8 5.9 - - - +
331C LYS* 3.0 29.9 + - - +
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Residues in contact with ARG 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C ALA* 3.0 38.7 + - - +
325C GLU* 3.7 27.1 + - - +
327C GLU* 1.3 77.1 - - - +
329C GLY* 1.3 61.5 + - - +
331C LYS* 3.3 10.6 + - + +
332C GLU* 3.0 46.0 + - + +
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Residues in contact with GLY 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.1 18.4 - - - -
109C LYS* 4.0 6.9 - - - -
112C LEU* 3.6 6.7 - - - -
325C GLU 2.8 17.5 + - - -
326C LEU 3.8 0.9 - - - -
328C ARG* 1.3 78.0 - - - +
330C LEU* 1.3 61.6 + - - +
332C GLU* 3.3 13.0 + - - +
333C ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ARG* 3.8 25.4 - - + +
58C LEU* 4.1 26.2 - - + -
63C LYS* 5.1 4.3 - - - +
112C LEU* 3.3 22.6 - - + +
116C LEU* 3.8 26.2 - - + -
326C LEU 2.9 17.4 + - - +
327C GLU* 3.8 8.3 - - - +
329C GLY* 1.3 74.4 - - - +
331C LYS* 1.3 63.9 + - - +
333C ALA* 3.2 3.1 + - - +
334C GLU* 3.0 48.2 + - - +
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C GLU 3.0 18.7 + - - +
328C ARG* 3.5 11.0 - - + +
330C LEU* 1.3 77.4 - - - +
332C GLU* 1.3 61.0 + - + +
334C GLU* 3.8 9.6 - - - +
335C GLU* 2.9 49.0 + - + +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 3.6 46.0 + - + +
328C ARG* 3.0 33.6 + - + +
329C GLY* 3.8 7.2 - - - +
331C LYS* 1.3 79.3 - - + +
333C ALA* 1.3 62.5 + - - +
335C GLU* 3.5 15.2 + - - +
336C ALA* 3.2 21.1 + - - +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 3.8 6.7 - - - +
112C LEU* 3.9 11.2 - - + +
113C GLY* 3.8 29.4 - - - +
116C LEU* 4.7 5.6 - - + -
118C THR* 2.8 27.1 + - - +
120C ALA* 3.8 11.0 - - - -
329C GLY 3.0 17.5 + - - +
330C LEU* 3.2 4.9 + - - +
332C GLU* 1.3 77.3 - - - +
334C GLU* 1.3 61.5 + - - +
336C ALA* 3.3 7.4 + - - +
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Residues in contact with GLU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LYS* 2.6 42.8 + - - +
116C LEU* 3.7 15.7 - - + -
118C THR* 4.5 8.3 - - - +
330C LEU* 3.0 36.4 + - + +
331C LYS* 3.9 7.3 - - - +
333C ALA* 1.3 75.7 - - - +
335C GLU* 1.3 63.9 + - - +
337C GLY* 3.2 14.7 + - - -
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Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C LYS* 2.9 40.3 + - + +
332C GLU* 3.6 15.4 - - - +
334C GLU* 1.3 78.6 - - - +
336C ALA* 1.3 61.2 + - - +
337C GLY* 3.1 2.4 + - - -
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 4.0 1.1 - - - +
119C LYS* 3.7 21.2 - - + +
120C ALA* 3.4 34.8 - - + +
332C GLU 3.2 9.2 + - - +
333C ALA 3.4 14.1 - - - +
334C GLU 3.1 0.8 - - - -
335C GLU* 1.3 76.0 - - - +
337C GLY* 1.3 61.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il