Contacts of the helix formed by residues 310 - 334 (chain C) in PDB entry 3DUF
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 SER 310 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLU* 5.5 2.0 - - - -
309C TRP* 1.3 85.6 + - - +
311C GLU* 1.3 64.7 + - - +
312C GLU* 2.9 18.6 + - - +
313C GLU* 3.0 33.3 + - - +
314C GLU 3.3 7.6 + - - -
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLU* 5.7 1.2 + - - -
310C SER* 1.3 72.1 - - - +
312C GLU* 1.3 61.1 + - + +
313C GLU 3.4 0.2 - - - -
314C GLU* 3.8 11.6 - - - +
315C ASN* 2.9 45.2 + - - +
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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 SER* 2.9 13.1 - - - +
311C GLU* 1.3 84.4 - - + +
313C GLU* 1.3 60.5 + - + +
315C ASN* 3.6 4.8 + - - +
316C ASN* 3.0 35.7 + - - +
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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
----------------------------------------------------------
47C LYS* 3.0 33.2 + - - +
51C ARG* 4.8 8.1 + - + +
308C LEU 4.0 5.5 - - - +
309C TRP* 3.6 25.9 + - + -
310C SER* 3.0 32.6 + - - +
312C GLU* 1.3 78.7 - - + +
314C GLU* 1.3 61.2 + - - +
316C ASN* 3.4 10.6 + - - +
317C VAL* 3.1 30.8 + - + +
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Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 4.1 0.9 - - - +
54C VAL* 4.1 21.2 - - + +
300C ARG* 3.2 38.6 + - - -
309C TRP* 2.7 45.0 + - + +
310C SER 3.3 5.2 + - - +
311C GLU* 3.8 12.5 - - - +
312C GLU 3.3 0.4 - - - -
313C GLU* 1.3 77.6 - - - +
315C ASN* 1.3 62.8 + - - +
317C VAL* 3.2 5.3 + - - +
318C ILE* 2.9 37.3 + - + +
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Residues in contact with ASN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C GLU* 2.9 31.1 + - - +
312C GLU* 4.2 6.0 - - - +
313C GLU 3.4 0.2 - - - -
314C GLU* 1.3 77.9 - - - +
316C ASN* 1.3 62.9 + - - +
318C ILE* 3.3 12.7 + - - +
319C GLU* 2.8 47.8 + - - +
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Residues in contact with ASN 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 3.0 24.6 + - - +
313C GLU* 3.6 11.9 - - - +
314C GLU 3.2 0.4 - - - -
315C ASN* 1.3 80.0 - - - +
317C VAL* 1.3 59.5 + - + +
319C GLU* 3.8 9.4 - - - +
320C GLN* 3.1 27.6 + - - +
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 3.6 55.9 - - + +
54C VAL* 3.8 18.2 - - + -
55C TYR* 4.3 14.3 - - + -
309C TRP* 4.5 4.9 - - + -
313C GLU* 3.1 17.2 + - + +
314C GLU* 3.5 7.0 - - - +
315C ASN 3.1 0.2 - - - -
316C ASN* 1.3 79.4 - - + +
318C ILE* 1.3 59.2 + - - +
319C GLU 3.2 0.2 - - - -
320C GLN* 3.8 14.1 - - - +
321C ALA* 2.9 27.9 + - - +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.6 26.0 - - + -
58C ILE* 3.7 30.7 - - + -
314C GLU* 2.9 32.6 + - + +
315C ASN* 3.3 19.3 + - + +
317C VAL* 1.3 78.1 - - - +
319C GLU* 1.3 61.3 + - - +
321C ALA* 3.4 5.7 + - - +
322C LYS* 3.0 53.0 + - + +
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Residues in contact with GLU 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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315C ASN* 2.8 40.4 + - - +
316C ASN* 3.8 10.6 - - - +
318C ILE* 1.3 82.0 - - - +
320C GLN* 1.3 66.3 + - - +
321C ALA 3.1 0.2 + - - -
322C LYS* 3.3 6.1 + - - +
323C GLU* 3.0 25.4 + - - +
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Residues in contact with GLN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 5.5 4.5 - - - -
55C TYR* 4.7 10.7 - - + -
316C ASN 3.1 15.1 + - - +
317C VAL* 3.8 20.2 - - - +
318C ILE 3.5 0.2 - - - -
319C GLU* 1.3 78.7 - - - +
321C ALA* 1.3 62.1 + - - +
323C GLU* 3.7 6.7 + - - +
324C GLU* 3.1 46.2 + - + +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 4.1 30.7 - - + -
58C ILE* 3.6 26.9 - - + -
317C VAL 2.9 19.5 + - - +
318C ILE* 3.5 6.1 - - - +
320C GLN* 1.3 74.4 - - - +
322C LYS* 1.3 68.2 + - - +
324C GLU* 3.2 3.8 + - - +
325C ILE* 2.9 29.9 + - + +
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Residues in contact with LYS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 4.2 17.3 - - + -
61C GLN* 6.0 0.2 - - - -
62C ARG* 3.9 30.6 + - + +
318C ILE* 3.0 35.6 + - + +
319C GLU* 3.8 5.8 - - - +
321C ALA* 1.3 76.2 - - - +
323C GLU* 1.3 62.7 + - - +
325C ILE* 3.2 8.7 + - - +
326C LYS* 3.0 26.1 + - - +
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Residues in contact with GLU 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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319C GLU 3.0 17.2 + - - +
320C GLN* 3.7 7.1 - - - +
322C LYS* 1.3 76.8 - - - +
324C GLU* 1.3 76.3 + - - +
326C LYS* 3.3 11.7 - - - +
327C GLU* 3.2 34.8 + - - +
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Residues in contact with GLU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 2.9 29.9 + - - +
115C LEU* 4.4 7.2 - - + +
320C GLN* 3.1 40.3 + - + +
321C ALA 3.7 1.3 - - - +
323C GLU* 1.3 86.3 - - - +
325C ILE* 1.3 67.7 + - - +
327C GLU* 3.0 8.0 + - + +
328C ALA* 2.9 23.2 + - - +
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Residues in contact with ILE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 4.9 8.3 - - + +
58C ILE* 5.0 3.1 - - + -
59C LEU* 3.4 37.0 - - + -
62C ARG* 4.0 37.7 - - + +
66C LEU* 4.1 19.3 - - + -
115C LEU* 3.6 18.6 - - + -
119C PHE* 4.0 8.0 - - + -
321C ALA* 2.9 30.3 + - + +
322C LYS* 3.5 9.4 - - - +
324C GLU* 1.3 75.0 - - - +
326C LYS* 1.3 64.1 + - - +
328C ALA* 3.3 2.8 + - - +
329C ILE* 3.1 23.6 + - + +
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Residues in contact with LYS 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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62C ARG* 6.1 2.5 - - - +
322C LYS 3.0 13.5 + - - +
323C GLU* 3.3 14.4 - - - +
325C ILE* 1.3 79.6 - - - +
327C GLU* 1.3 66.2 + - - +
329C ILE* 3.6 9.9 + - + +
330C LYS* 3.3 20.3 + - - +
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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
----------------------------------------------------------
323C GLU* 3.2 27.7 + - - +
324C GLU* 3.0 11.4 + - + +
326C LYS* 1.3 84.0 - - + +
328C ALA* 1.3 65.7 + - - +
329C ILE 3.2 0.4 - - - -
330C LYS* 3.3 11.8 + - - +
331C LYS* 3.0 35.0 + - + +
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.7 18.8 - - + -
116C TYR* 3.5 25.9 - - - +
119C PHE* 3.4 29.2 - - + -
324C GLU 2.9 11.9 + - - +
325C ILE 3.3 3.8 + - - +
327C GLU* 1.3 75.6 - - - +
329C ILE* 1.3 58.3 + - - +
331C LYS* 3.3 2.3 + - - -
332C ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 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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66C LEU* 3.8 30.1 - - + -
71C ARG* 3.4 37.7 - - + +
72C LEU* 4.7 7.2 - - + -
119C PHE* 4.1 16.4 - - + -
123C ARG* 3.5 26.7 - - - +
325C ILE 3.1 16.3 + - - +
326C LYS* 3.7 10.3 - - + +
327C GLU 3.2 0.2 - - - -
328C ALA* 1.3 78.6 - - - +
330C LYS* 1.3 63.0 + - + +
332C ALA* 3.5 2.5 + - + +
333C ASP* 3.0 34.4 + - - +
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Residues in contact with LYS 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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326C LYS 3.3 11.7 + - - +
327C GLU* 3.3 16.8 + - - +
329C ILE* 1.3 81.3 - - + +
331C LYS* 1.3 61.6 + - + +
333C ASP* 3.4 10.2 + - - +
334C GLU* 3.0 35.2 + - - +
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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
----------------------------------------------------------
116C TYR* 3.8 50.6 + - + -
327C GLU* 3.0 27.7 + - + +
328C ALA* 3.5 5.4 - - - +
330C LYS* 1.3 76.5 - - + +
332C ALA* 1.3 63.0 + - - +
334C GLU* 3.5 24.0 + - - +
335C THR* 3.2 14.9 + - - -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C TYR* 4.1 9.8 - - - +
119C PHE* 4.5 10.5 - - + -
120C LEU* 3.8 28.8 - - + +
123C ARG* 3.8 20.6 + - - +
328C ALA 3.0 15.5 + - - +
329C ILE* 4.0 6.1 - - - +
330C LYS 3.4 0.2 - - - -
331C LYS* 1.3 75.9 - - - +
333C ASP* 1.3 61.0 + - - +
335C THR* 3.4 22.5 - - - +
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 4.9 3.6 + - - -
123C ARG* 2.6 44.1 + - - +
329C ILE* 3.0 24.4 + - - +
330C LYS* 3.7 10.6 - - - +
331C LYS 3.2 0.2 - - - -
332C ALA* 1.3 74.8 - - - +
334C GLU* 1.3 60.9 + - + +
335C THR 3.1 12.4 + - - +
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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
----------------------------------------------------------
330C LYS* 3.0 26.7 + - + +
331C LYS* 3.9 22.5 - - - +
332C ALA 3.4 0.4 - - - -
333C ASP* 1.3 74.7 - - + +
335C THR* 1.3 62.4 + - - +
336C PRO* 3.4 8.8 - - - +
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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