Contacts of the helix formed by residues 321 - 343 (chain C) in PDB entry 2VT4
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 PRO 321 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU 4.4 2.2 - - - +
320C VAL* 1.3 92.9 - - + +
322C ASP* 1.3 54.9 + - - +
323C TRP* 3.0 36.3 - - + +
324C LEU* 2.8 43.4 + - + +
325C PHE* 3.2 8.0 + - - -
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Residues in contact with ASP 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ASN* 5.8 2.3 + - - -
320C VAL 3.6 4.5 + - - +
321C PRO* 1.3 69.6 - - - +
323C TRP* 1.3 56.8 + - - +
325C PHE* 3.0 16.9 - - - +
326C VAL* 3.0 30.0 + - + +
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Residues in contact with TRP 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PRO* 2.8 36.0 + - + +
322C ASP* 1.3 77.1 - - - +
324C LEU* 1.3 92.2 + - + +
326C VAL* 3.2 9.8 + - - +
327C ALA* 2.8 36.9 + - + +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C VAL* 5.3 0.2 - - + -
320C VAL* 3.9 23.1 - - + -
321C PRO* 2.8 24.9 + - + +
323C TRP* 1.3 99.0 - - + +
325C PHE* 1.3 66.6 + - - +
326C VAL 3.2 0.2 - - - -
327C ALA* 3.9 9.0 - - + -
328C PHE* 3.0 62.8 + - + +
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Residues in contact with PHE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PHE* 4.0 25.7 - + - -
309C VAL* 3.3 39.9 - - + -
310C ASN* 3.6 24.9 - - - -
313C ASN* 3.7 26.9 - - + -
320C VAL* 5.0 5.6 - - + +
321C PRO 3.2 6.2 + - - +
322C ASP* 3.0 27.6 + - - +
324C LEU* 1.3 77.8 - - - +
326C VAL* 1.3 63.3 + - + -
328C PHE* 3.5 3.7 + - - +
329C ASN* 3.3 19.3 + - + +
400C P32 5.2 9.9 - - + -
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 4.4 17.7 - - + -
322C ASP* 3.0 16.0 + - + +
323C TRP* 3.2 10.7 + - - +
325C PHE* 1.3 78.5 - - + +
327C ALA* 1.3 66.7 + - - +
329C ASN* 3.2 6.6 + - - +
330C TRP* 3.1 42.7 + - + +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TRP* 2.8 28.4 + - + +
324C LEU* 3.7 20.4 - - + +
326C VAL* 1.3 73.0 - - - +
328C PHE* 1.3 61.1 + - + +
330C TRP* 3.2 9.3 + - - +
331C LEU* 3.1 23.2 + - - +
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Residues in contact with PHE 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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302C CYS 4.3 1.9 - - - +
305C PRO* 3.7 33.4 - - + +
306C PHE* 4.1 22.6 + - + +
309C VAL* 3.7 30.3 - - + -
324C LEU* 3.0 49.5 + - + +
325C PHE* 3.9 4.3 - - - +
327C ALA* 1.3 74.2 - - + +
329C ASN* 1.3 66.3 + - - +
330C TRP 3.1 1.8 - - - -
331C LEU* 3.1 18.6 + - + +
332C GLY* 3.1 17.8 + - - -
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Residues in contact with ASN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C TRP* 3.7 7.8 - - - -
306C PHE* 3.6 24.6 - - + -
325C PHE* 3.3 7.9 + - + +
326C VAL* 3.2 12.1 + - - +
328C PHE* 1.3 78.3 - - - +
330C TRP* 1.3 60.3 + - + +
332C GLY* 3.2 2.1 + - - -
333C TYR* 3.1 38.9 + - - -
400C P32 2.6 60.6 + - - +
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Residues in contact with TRP 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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48C MET* 3.6 31.2 - - + -
51C VAL* 5.0 6.1 - - + -
95C VAL* 4.0 30.5 - - + -
98C GLY* 3.7 12.3 - - - -
99C ALA* 3.9 10.5 - - - -
102C VAL* 3.4 36.3 - - + +
326C VAL* 3.1 36.0 + - + +
327C ALA* 3.6 10.5 - - - +
328C PHE 3.1 0.6 - - - -
329C ASN* 1.3 79.2 - - + +
331C LEU* 1.3 57.8 + - - +
332C GLY 3.2 0.4 - - - -
333C TYR* 3.6 31.6 - + + +
334C ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 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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301C LEU 4.1 8.1 - - - +
302C CYS* 3.5 40.2 - - - +
305C PRO* 4.5 12.6 - - + -
327C ALA 3.1 11.7 + - - +
328C PHE* 3.1 24.1 + - + +
330C TRP* 1.3 76.9 - - - +
332C GLY* 1.3 63.4 + - - +
334C ALA* 3.5 5.0 + - + +
335C ASN 3.4 15.4 + - - -
338C MET* 4.8 9.4 - - + -
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Residues in contact with GLY 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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302C CYS 3.3 11.3 + - - -
303C TRP* 3.3 43.5 + - - -
328C PHE 3.1 10.5 + - - -
329C ASN 3.2 3.8 + - - -
330C TRP 3.2 0.2 - - - -
331C LEU* 1.3 77.0 - - - +
333C TYR* 1.3 61.2 + - - +
335C ASN* 3.3 18.0 - - - +
336C SER* 4.3 1.9 + - - -
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Residues in contact with TYR 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 4.2 7.4 - - - +
90C VAL* 4.4 11.9 - - + +
94C VAL* 3.5 29.8 - - + +
95C VAL* 4.1 19.7 - - + -
98C GLY* 5.5 1.6 - - - -
117C TRP* 4.0 13.8 - + - -
121C ASP* 2.4 35.6 + - - -
125C VAL* 5.9 0.2 - - + -
303C TRP* 4.5 5.2 - + - -
329C ASN* 3.1 34.2 + - - -
330C TRP* 3.6 48.9 - + + +
331C LEU 3.3 0.2 - - - -
332C GLY* 1.3 78.4 - - - +
334C ALA* 1.3 62.2 + - - +
336C SER* 3.0 24.5 + - - -
400C P32 3.8 7.7 + - - +
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Residues in contact with ALA 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 5.4 3.6 - - - -
330C TRP* 3.0 16.8 + - - +
331C LEU* 3.8 10.5 - - + +
332C GLY 3.3 0.2 - - - -
333C TYR* 1.3 71.2 - - - +
335C ASN* 1.3 67.1 + - - +
336C SER 2.9 2.7 - - - -
337C ALA* 2.8 21.9 + - - +
338C MET* 3.6 22.0 + - + +
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Residues in contact with ASN 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP* 4.8 5.7 + - - -
295C ILE 5.1 0.9 - - - +
298C VAL* 3.5 19.4 - - - +
299C PHE* 3.4 47.6 + - - +
302C CYS* 3.7 15.0 - - + -
303C TRP* 4.4 4.2 - - - +
331C LEU 3.4 5.5 + - - -
332C GLY 3.3 15.3 - - - +
334C ALA* 1.3 76.9 - - - +
336C SER* 1.3 59.6 + - - +
337C ALA 2.8 6.4 + - - -
338C MET* 2.9 27.6 + - - +
339C ASN* 3.9 16.0 + - - +
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Residues in contact with SER 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 3.8 18.5 - - - +
59C ASN* 2.9 27.5 + - - -
87C ASP* 2.7 41.0 + - - +
90C VAL* 3.9 17.3 - - - +
332C GLY 4.3 1.6 + - - -
333C TYR* 3.0 16.2 + - - -
334C ALA 2.9 1.4 + - - -
335C ASN* 1.3 77.7 + - - +
337C ALA* 1.3 56.7 + - - +
339C ASN 4.9 1.3 - - - -
340C PRO* 4.4 1.4 - - - +
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Residues in contact with ALA 337 (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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51C VAL* 6.2 0.9 - - + -
54C LEU* 4.1 20.9 - - + +
55C ILE* 3.4 35.2 - - + +
334C ALA* 2.8 11.5 + - + +
336C SER* 1.3 78.3 - - - +
338C MET* 1.3 63.7 + - + +
339C ASN 3.4 2.2 - - - -
340C PRO* 3.7 12.3 - - - +
341C ILE* 3.4 19.4 + - + +
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Residues in contact with MET 338 (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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298C VAL* 3.5 21.3 - - + -
302C CYS* 3.5 33.7 - - - -
331C LEU* 4.8 8.1 - - + -
334C ALA* 3.9 27.8 - - + +
335C ASN* 2.9 12.5 + - - +
337C ALA* 1.3 80.2 - - - +
339C ASN* 1.3 59.2 + - - +
340C PRO 3.6 0.2 - - - -
341C ILE* 3.3 14.3 + - + +
342C ILE* 2.8 39.4 + - + +
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Residues in contact with ASN 339 (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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59C ASN* 4.8 2.4 + - - +
83C LEU* 3.9 22.2 - - - +
84C ALA* 5.6 0.6 - - - +
87C ASP* 3.6 23.6 + - - +
295C ILE* 3.4 30.9 - - - +
298C VAL* 6.0 1.0 - - - +
335C ASN* 3.9 17.0 + - - +
336C SER 5.2 0.7 - - - +
338C MET* 1.3 75.2 - - - +
340C PRO* 1.3 76.9 - - + +
342C ILE* 3.0 6.2 + - - +
343C TYR* 2.9 50.1 + - + -
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Residues in contact with PRO 340 (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 LEU 5.5 0.4 - - - +
58C GLY* 3.2 47.3 - - - +
59C ASN* 3.7 20.4 - - - +
61C LEU* 6.3 1.1 - - + -
62C VAL* 4.1 6.5 - - + -
336C SER 4.4 0.4 - - - +
337C ALA* 3.7 14.6 - - - +
339C ASN* 1.3 95.9 - - + +
341C ILE* 1.3 64.2 + - + +
343C TYR* 3.3 22.4 + - + +
344C CYS* 3.7 11.2 + - - -
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Residues in contact with ILE 341 (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 LEU* 5.1 20.9 - - + -
337C ALA 3.4 20.4 - - - +
338C MET* 3.3 16.3 + - + +
339C ASN 3.1 0.6 - - - -
340C PRO* 1.3 79.2 - - + +
342C ILE* 1.3 67.3 + - + +
344C CYS* 3.0 30.2 + - + +
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Residues in contact with ILE 342 (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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291C THR* 4.4 11.3 - - + +
294C ILE* 3.6 37.5 - - + -
295C ILE* 3.7 29.6 - - + +
298C VAL* 3.9 24.7 - - + -
338C MET* 2.8 28.1 + - + +
339C ASN* 3.6 7.0 - - - +
341C ILE* 1.3 71.9 - - + +
343C TYR* 1.3 57.7 - - - +
344C CYS 2.9 11.0 + - - -
345C ARG* 3.1 29.4 + - - +
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Residues in contact with TYR 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 6.0 0.4 - - - -
62C VAL* 3.7 32.3 - - + -
80C ILE* 3.0 48.7 + - + +
83C LEU* 4.4 2.4 - - - +
84C ALA* 6.3 0.4 - - + -
291C THR* 4.2 18.6 - - + -
292C LEU* 5.6 0.9 - - + -
295C ILE* 3.7 26.1 - - + +
339C ASN* 2.9 43.4 + - + -
340C PRO* 3.7 7.2 - - + +
341C ILE 3.2 0.6 - - - -
342C ILE* 1.3 75.5 - - - +
344C CYS* 1.3 57.3 + - - +
345C ARG 3.0 6.4 + - - -
346C SER* 3.2 20.9 + - - +
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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