Contacts of the helix formed by residues 31 - 44 (chain B) in PDB entry 3V3Q
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 ALA 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PRO* 1.3 78.7 + - + -
32B ASN* 1.3 55.9 + - - +
33B LEU 3.6 2.5 - - - +
34B LEU* 3.3 18.6 + - + +
35B THR* 2.7 35.8 + - - -
206B GLU* 5.8 3.1 - - - +
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 1.3 72.4 - - - +
33B LEU* 1.3 66.4 + - - +
35B THR* 4.2 4.8 - - - +
36B SER* 3.2 30.2 + - - -
94B PRO* 5.3 0.5 - - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 5.0 0.8 - - - +
32B ASN* 1.3 76.3 - - - +
34B LEU* 1.3 66.7 + - - +
35B THR 3.2 0.3 + - - -
36B SER* 3.2 3.8 + - - -
37B LEU* 3.0 42.7 + - + +
93B ILE* 5.9 0.4 - - + -
94B PRO* 4.1 31.0 - - + +
196B LEU* 6.0 1.6 - - + -
199B ARG* 3.4 42.6 - - + +
200B ILE* 4.2 10.8 - - + -
203B CYS* 3.8 18.2 - - + -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO 4.1 14.1 - - - +
31B ALA* 3.3 18.0 + - + +
33B LEU* 1.3 78.4 - - - +
35B THR* 1.3 57.4 + - - +
37B LEU* 3.6 5.0 + - + +
38B VAL* 3.1 35.0 + - + +
170B PRO* 3.7 27.6 - - + +
174B CYS* 3.5 30.7 - - - -
203B CYS* 3.5 18.4 - - - +
207B HIS* 3.7 35.0 - - + +
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO 3.4 22.7 + - - -
31B ALA 2.7 26.3 + - - -
32B ASN* 4.2 5.2 - - - +
34B LEU* 1.3 70.7 - - - +
36B SER* 1.3 62.9 + - - +
38B VAL* 3.9 7.5 - - + +
39B ARG* 3.0 31.5 + - + +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 3.2 26.1 + - - -
33B LEU 3.8 0.7 - - - -
35B THR* 1.3 74.4 - - - +
37B LEU* 1.3 59.7 + - - +
39B ARG* 3.3 23.4 + - - +
40B ALA* 2.8 29.4 + - - +
92B LYS 4.6 1.1 - - - +
94B PRO* 3.6 32.3 - - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.0 43.9 + - + +
34B LEU* 3.7 4.3 - - - +
36B SER* 1.3 76.2 - - - +
38B VAL* 1.4 53.7 + - - +
40B ALA* 3.0 7.0 + - - +
41B HIS* 2.8 34.7 + - - +
89B TRP* 4.8 2.5 + - + +
93B ILE* 4.1 26.9 - - + -
94B PRO* 4.6 2.5 - - + -
173B ALA* 3.8 17.3 - - + +
174B CYS* 3.9 32.1 - - - -
177B ALA* 3.9 23.3 - - + -
200B ILE* 4.4 12.6 - - + -
203B CYS* 4.4 2.9 - - - -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.1 23.4 + - + +
35B THR* 3.9 7.4 - - + +
36B SER 3.3 0.4 - - - -
37B LEU* 1.4 74.7 - - - +
39B ARG* 1.3 60.8 + - - +
41B HIS* 3.2 2.3 + - - +
42B LEU* 2.9 43.3 + - + +
169B VAL* 4.1 15.7 - - + -
170B PRO* 3.5 44.0 - - + -
173B ALA* 3.8 8.1 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B THR* 3.0 21.4 + - + +
36B SER* 3.5 37.9 + - - +
38B VAL* 1.3 76.6 - - - +
40B ALA* 1.3 68.5 + - - +
42B LEU* 4.7 5.8 - - - +
43B ASP* 3.0 49.0 + - - +
92B LYS* 3.5 46.8 + - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER 2.8 19.6 + - - +
37B LEU* 3.6 6.1 - - - +
39B ARG* 1.3 76.9 - - - +
41B HIS* 1.3 66.9 + - - +
43B ASP* 3.9 1.4 - - - +
44B SER* 3.2 14.2 + - - -
89B TRP* 3.3 27.9 - - + +
92B LYS* 3.6 44.7 + - + +
93B ILE* 4.8 2.9 - - + +
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Residues in contact with HIS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 2.8 12.0 + - - +
38B VAL 3.5 5.6 - - - +
40B ALA* 1.3 75.1 - - - +
42B LEU* 1.3 74.7 + - + +
44B SER* 2.7 21.9 + - - -
89B TRP* 3.6 15.7 + - - +
119B ARG* 4.5 11.3 + - + -
122B TYR* 4.2 8.4 - + - -
169B VAL* 3.9 29.5 - - + +
172B PHE* 3.5 36.4 - + - -
173B ALA* 4.1 13.9 - - + -
176B SER* 5.0 2.6 + - - +
301B GOL 2.8 49.5 + - - -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 2.9 36.4 + - + +
39B ARG* 4.4 4.0 - - - +
41B HIS* 1.3 80.3 - - + +
43B ASP* 1.3 63.9 + - - +
44B SER 3.4 0.3 + - - -
45B GLY 3.6 15.1 + - - +
169B VAL* 4.5 14.4 - - + -
301B GOL 3.8 32.6 + - - +
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 3.0 46.7 + - - +
40B ALA 4.0 2.7 - - - +
42B LEU* 1.3 78.5 - - - +
44B SER* 1.3 56.7 + - - +
45B GLY 3.3 7.9 + - - +
92B LYS* 4.0 24.1 + - - +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA 3.2 11.6 + - - -
41B HIS* 2.7 21.4 + - - -
43B ASP* 1.3 76.3 - - - +
45B GLY* 1.3 54.4 + - - +
85B VAL* 3.1 19.8 - - - +
89B TRP* 3.8 19.2 - - - -
119B ARG* 2.7 50.6 + - - -
134B CYS* 4.3 3.1 - - - +
301B GOL 4.5 0.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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