Contacts of the helix formed by residues 31 - 47 (chain H) in PDB entry 2WWA
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 ARG 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PRO* 3.6 17.1 + - + +
30H ILE* 1.4 79.8 - - - +
32H PRO* 1.3 64.9 - - + +
33H ASP* 3.3 42.9 + - - +
34H ILE* 3.6 33.3 - - + +
35H VAL* 3.7 19.2 + - - +
124H SER* 5.8 8.5 - - - -
244H LEU* 5.5 0.2 - - - +
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Residues in contact with PRO 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE 4.2 5.4 - - - +
31H ARG* 1.3 88.7 - - + +
33H ASP* 1.4 70.0 + - + +
34H ILE 3.4 0.4 - - - -
35H VAL* 3.5 7.0 + - + +
36H HIS* 3.2 23.4 + - - +
242H ALA 5.2 0.2 - - - +
244H LEU* 3.7 33.8 - - + +
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Residues in contact with ASP 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ARG* 3.3 40.8 + - - +
32H PRO* 1.4 83.6 - - + +
34H ILE* 1.4 74.5 + - - +
36H HIS* 3.5 5.6 + - - +
37H THR* 2.9 29.8 + - - +
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Residues in contact with ILE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ARG* 3.6 30.2 + - + +
32H PRO 3.4 0.2 - - - -
33H ASP* 1.4 86.2 + - - +
35H VAL* 1.4 65.1 + - - +
37H THR* 3.3 6.7 + - - -
38H VAL* 3.1 37.6 + - + +
120H TYR* 5.9 4.0 - - + -
121H ALA* 5.1 5.4 - - - +
124H SER* 4.2 22.9 - - - +
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Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ILE* 6.4 0.4 - - + -
31H ARG 3.7 15.6 + - - +
32H PRO 3.5 9.8 + - - +
33H ASP 3.3 0.4 - - - -
34H ILE* 1.4 79.8 - - - +
36H HIS* 1.4 60.6 - - - +
38H VAL 3.9 0.2 + - - -
39H PHE* 3.4 21.8 + - - +
124H SER* 5.4 6.1 - - - +
125H ALA* 5.2 3.8 - - - -
128H ALA* 5.1 15.0 - - + -
235H LEU* 3.7 42.9 - - + +
239H ALA* 5.4 2.5 - - + -
242H ALA* 3.7 27.7 - - + +
244H LEU* 4.0 22.9 - - + +
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Residues in contact with HIS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H PRO 3.2 16.9 + - - +
33H ASP* 3.9 5.8 - - - +
35H VAL* 1.4 75.4 - - + +
37H THR* 1.4 61.9 + - - +
39H PHE* 3.4 6.4 + + - +
40H THR* 3.1 31.7 + - - +
241H GLY 4.4 6.5 + - - -
242H ALA* 3.6 30.9 - - + +
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Residues in contact with THR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ASP* 2.9 20.3 + - - +
34H ILE* 3.3 6.7 + - - -
36H HIS* 1.4 76.1 - - - +
38H VAL* 1.4 63.3 + - + +
40H THR* 3.3 12.2 - - + +
41H SER* 2.9 33.7 + - - +
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 3.1 27.4 + - + +
37H THR* 1.4 74.4 - - + +
39H PHE* 1.4 63.6 + - - +
41H SER* 3.3 15.9 + - - -
42H VAL* 3.4 23.9 + - + +
117H GLU 5.5 0.4 - - - +
121H ALA* 3.7 29.6 - - + -
235H LEU* 3.9 26.2 - - + -
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Residues in contact with PHE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H VAL 3.4 17.9 + - - +
36H HIS* 3.4 10.5 + + - +
37H THR 3.3 0.4 - - - -
38H VAL* 1.4 78.4 - - - +
40H THR* 1.4 59.6 + - - +
42H VAL* 3.2 20.4 - - - +
43H ASN* 2.9 30.8 - - + +
235H LEU* 3.9 25.1 - - + +
236H LEU* 4.0 35.0 - - + -
239H ALA 4.1 4.5 - - - -
240H PRO* 4.2 2.0 - - + -
241H GLY* 3.3 34.3 - - - -
242H ALA* 3.9 18.4 - - + -
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Residues in contact with THR 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H HIS* 3.1 25.1 + - + +
37H THR* 3.3 20.6 - - + +
39H PHE* 1.4 75.8 - - - +
41H SER* 1.4 64.4 + - - +
43H ASN* 3.3 26.7 + - - -
44H LYS* 3.3 30.3 + - - +
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Residues in contact with SER 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR* 2.9 25.5 + - - +
38H VAL* 3.5 12.8 - - - -
39H PHE 3.3 0.6 - - - -
40H THR* 1.4 79.9 - - - +
42H VAL* 1.4 63.2 + - - +
44H LYS* 3.6 16.4 + - - +
45H ASN* 3.3 23.7 + - - +
111H VAL* 3.6 34.9 + - - +
113H VAL* 6.1 4.0 - - - -
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H VAL* 3.4 20.2 + - + +
39H PHE* 3.2 22.0 - - + +
41H SER* 1.4 80.3 - - - +
43H ASN* 1.4 59.6 + - - +
45H ASN* 3.6 26.1 + - - +
46H LYS* 3.9 5.2 + - - +
113H VAL* 5.7 8.7 - - + -
235H LEU* 6.4 1.1 - - + -
236H LEU* 3.9 32.1 - - + -
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Residues in contact with ASN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H PHE* 2.9 40.2 - - - +
40H THR* 3.3 19.9 + - - +
42H VAL* 1.4 79.1 - - + +
44H LYS* 1.4 67.5 + - - +
45H ASN 3.3 0.2 - - - -
46H LYS* 3.4 8.1 + - - +
47H ARG* 3.1 46.5 + - + +
236H LEU* 5.5 8.7 - - + -
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H THR* 3.3 37.6 + - - +
41H SER* 3.8 4.5 + - - +
42H VAL 3.4 0.4 - - - -
43H ASN* 1.4 84.0 - - - +
45H ASN* 1.4 65.4 + - - +
47H ARG* 3.4 22.1 + - - +
109H TRP* 3.5 62.5 - - + +
110H ASN* 4.7 14.7 + - - +
111H VAL* 3.7 29.6 - - - +
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Residues in contact with ASN 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H SER 3.3 20.9 + - - +
42H VAL* 3.6 18.6 + - - +
43H ASN 3.3 0.2 - - - -
44H LYS* 1.4 77.5 - - - +
46H LYS* 1.4 60.2 + - - +
47H ARG 4.3 1.9 - - - +
110H ASN* 3.4 27.5 - - + +
111H VAL 3.4 17.5 + - - +
113H VAL* 5.5 6.1 - - - +
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H VAL 3.9 4.2 + - - +
43H ASN* 3.4 12.6 + - - +
44H LYS 3.3 0.2 - - - -
45H ASN* 1.4 79.6 - - - +
47H ARG* 1.4 67.6 + - + +
48H GLN* 3.7 17.2 + - - +
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Residues in contact with ARG 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ASN* 3.1 35.3 + - + +
44H LYS* 3.4 17.1 + - - +
45H ASN 4.3 2.1 - - - +
46H LYS* 1.4 82.5 - - + +
48H GLN* 1.3 67.5 + - - +
195H ARG* 3.2 42.2 + - - +
196H ASN* 4.0 9.7 + - - +
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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