Contacts of the helix formed by residues 30 - 41 (chain B) in PDB entry 3W96
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 THR 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.9 23.1 - - - +
27B GLN 4.2 5.6 - - - +
28B GLY* 2.8 21.4 + - - +
29B ILE* 1.3 76.6 - - - +
31B LYS* 1.3 66.0 + - - +
32B PRO* 3.2 24.8 - - - +
33B ALA* 3.1 21.8 + - - +
34B ILE* 3.3 10.4 + - - +
55B ARG* 4.3 1.3 - - - +
60I C 3.5 28.9 + - - +
61I A 3.8 11.0 - - - +
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Residues in contact with LYS 31 (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 THR* 1.3 71.9 - - - +
32B PRO* 1.3 69.6 - - + +
34B ILE* 3.3 4.3 + - - +
35B ARG* 3.0 27.6 + - + +
48B GLY* 5.8 1.2 - - - -
51B TYR* 3.3 56.9 + - + +
55B ARG* 3.4 20.6 - - - +
61I A 4.3 4.4 + - - +
227J G 6.3 1.0 - - - +
228J A 5.7 2.1 + - - -
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Residues in contact with PRO 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.2 17.3 - - - +
31B LYS* 1.3 96.4 - - + +
33B ALA* 1.3 55.9 + - - +
35B ARG* 3.8 22.5 + - - +
36B ARG* 2.9 29.9 + - - +
60I C 3.8 32.1 - - + +
61I A 3.1 24.5 - - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 3.3 20.0 - - - +
62A ILE* 4.4 14.8 - - + -
63A ARG* 5.2 3.8 - - + -
29B ILE* 5.3 1.3 - - + -
30B THR* 3.1 21.9 + - - +
31B LYS 3.1 0.6 - - - -
32B PRO* 1.3 78.3 - - - +
34B ILE* 1.3 68.1 + - + +
36B ARG* 3.0 23.3 + - - +
37B LEU* 2.9 23.6 + - - +
60I C 4.8 1.1 - - - +
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Residues in contact with ILE 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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100A LEU* 6.1 0.4 - - + -
104A PHE* 4.1 22.9 - - + -
29B ILE* 4.1 24.2 - - + +
30B THR 3.6 9.0 - - - +
31B LYS 3.3 6.7 + - - +
33B ALA* 1.3 73.2 - - - +
35B ARG* 1.3 58.9 + - - +
37B LEU* 2.6 37.0 + - + +
38B ALA* 2.8 11.4 + - + -
46B ILE* 5.9 0.4 - - + -
50B ILE* 4.6 2.5 - - + -
51B TYR* 3.8 46.7 - - + +
54B THR* 4.1 20.2 - - + +
55B ARG* 4.1 18.4 - - + +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 3.0 39.6 + - - -
54A TYR* 5.5 0.6 + - - -
31B LYS* 3.0 18.7 + - - +
32B PRO* 3.8 27.4 + - - +
34B ILE* 1.3 78.3 - - - +
36B ARG* 1.3 65.9 + - - +
38B ALA* 3.1 3.3 + - - +
39B ARG* 2.8 60.2 + - - +
46B ILE* 3.6 30.3 - - + -
51B TYR* 3.9 16.1 - - - +
228J A 5.4 6.7 - - - +
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 2.9 41.5 + - + +
61A LEU* 2.9 57.7 + - + +
62A ILE* 4.8 3.4 - - - +
63A ARG* 5.1 2.8 - - - +
32B PRO* 2.9 37.0 + - - +
33B ALA* 3.0 19.8 + - - +
35B ARG* 1.3 84.5 - - - +
37B LEU* 1.3 52.5 + - - +
39B ARG* 2.7 29.5 + - - +
40B ARG 3.0 10.7 + - - -
59I G 5.7 2.5 - - - -
60I C 3.5 30.6 + - - -
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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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61A LEU* 4.1 15.7 - - + -
62A ILE* 3.9 19.5 - - + -
97A GLU* 3.7 33.9 - - + +
100A LEU* 3.4 36.6 - - + -
101A VAL* 3.9 24.4 - - + +
104A PHE* 3.9 15.4 - - + -
29B ILE* 5.8 0.2 - - + -
33B ALA 2.9 14.3 + - - +
34B ILE* 2.6 22.3 + - + +
36B ARG* 1.3 70.2 - - - +
38B ALA* 1.3 63.7 + - - +
39B ARG 3.0 0.9 + - - -
40B ARG* 3.2 5.2 + - - +
41B GLY* 3.1 16.6 + - - -
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Residues in contact with ALA 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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104A PHE* 3.6 38.0 - - + -
34B ILE* 2.8 13.3 + - + +
35B ARG* 3.6 7.4 - - - +
37B LEU* 1.3 73.3 - - - +
39B ARG* 1.3 59.3 + - - +
41B GLY 3.5 0.9 + - - -
42B GLY 3.4 3.5 + - - -
43B VAL* 2.8 38.5 + - + +
46B ILE* 3.6 26.5 - - + -
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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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47A ALA* 3.9 19.8 - - - +
50A GLU* 3.6 36.4 + - + +
51A ILE* 3.1 31.7 - - - +
54A TYR* 3.9 16.2 - - + -
55A GLN* 4.2 0.2 - - - +
35B ARG* 2.8 55.2 + - - +
36B ARG* 2.7 15.3 + - - +
38B ALA* 1.3 75.8 - - - +
40B ARG* 1.3 57.8 + - - +
41B GLY 3.1 1.6 - - - -
42B GLY* 2.8 14.9 + - - -
43B VAL 3.1 23.4 + - - -
44B LYS 3.6 12.7 + - - -
46B ILE* 3.8 24.2 - - - +
228J A 4.6 10.9 + - - +
229J A 4.5 6.9 + - - -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 2.9 25.8 + - + +
55A GLN* 3.3 28.3 + - - +
57A SER* 2.6 47.1 + - - -
58A THR* 4.2 4.4 - - - +
59A GLU 2.8 28.1 + - - +
60A LEU* 5.8 0.4 - - - +
61A LEU* 3.4 27.3 - - + +
97A GLU* 4.4 5.7 + - - -
101A VAL* 3.8 29.2 - - + +
105A GLU* 4.7 1.4 - - - +
36B ARG 3.0 9.2 + - - +
37B LEU* 3.2 8.9 + - - +
39B ARG* 1.3 70.7 - - - +
41B GLY* 1.3 57.3 + - - +
42B GLY 2.8 9.7 + - - -
106G GLY* 5.1 5.2 - - - -
107G VAL* 3.8 25.6 - - + +
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Residues in contact with GLY 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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55A GLN* 4.5 2.0 - - - -
101A VAL* 3.7 26.8 - - - +
104A PHE* 4.3 5.4 - - - -
105A GLU* 3.7 26.7 + - - +
108A ASN* 4.5 3.5 - - - +
37B LEU 3.1 10.7 + - - -
38B ALA 3.7 5.2 - - - -
39B ARG 3.1 0.8 - - - -
40B ARG* 1.3 75.0 - - - +
42B GLY* 1.3 62.2 + - - +
43B VAL* 3.5 6.1 - - - +
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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