Contacts of the helix formed by residues 100 - 114 (chain B) in PDB entry 3W31
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 GLN 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY* 3.5 16.3 + - - +
62A ALA* 4.5 8.1 - - - +
143A ALA 4.1 4.7 + - - +
144A THR* 2.7 34.4 + - - +
145A HIS* 4.3 4.0 - - - +
146A TRP* 5.7 1.3 - - - -
170A TYR* 3.4 22.3 + - - -
7B ARG* 3.5 17.5 - - - +
11B GLU* 3.1 14.6 - - - +
14B ARG* 4.2 8.1 - - - +
62B TYR* 3.8 2.2 - - - -
95B TRP* 4.2 9.8 - - - -
98B ALA 3.4 12.5 - - - +
99B LEU* 1.3 79.2 - - - +
101B ILE* 1.3 66.6 - - - +
102B ARG* 3.3 6.7 - - + +
103B THR* 3.1 25.5 + - - +
104B VAL* 3.7 2.6 + - - +
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Residues in contact with ILE 101 (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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11B GLU* 3.2 22.4 + - + +
12B THR* 6.4 0.7 - - - -
15B LEU* 4.5 11.2 - - + -
35B PHE* 6.0 0.7 - - + -
56B LEU* 3.9 22.9 - - + -
58B LEU* 3.4 37.2 - - + -
62B TYR* 3.7 22.9 + - + +
67B PRO* 5.1 6.7 - - + -
100B GLN* 1.3 71.9 - - - +
102B ARG* 1.3 68.5 + - - +
104B VAL* 2.9 12.2 + - + +
105B LEU* 2.9 46.2 + - + -
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Residues in contact with ARG 102 (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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58A GLY 5.7 2.0 - - - -
59A ASP 5.5 2.7 - - - +
170A TYR* 4.1 24.8 - - - +
172A PRO* 6.2 2.6 - - - +
11B GLU* 4.7 0.8 + - - -
14B ARG* 3.6 38.9 - - - +
18B GLU 2.8 29.3 + - - -
19B PRO 3.7 1.2 - - - -
20B VAL* 3.6 39.4 - - + +
21B PRO* 5.4 3.0 - - - +
100B GLN* 3.3 3.5 - - + +
101B ILE* 1.3 78.7 - - - +
103B THR* 1.3 53.4 + - - +
105B LEU* 3.8 2.9 - - - +
106B LEU* 2.7 54.3 + - + +
201B IOD 3.7 19.6 - - + +
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Residues in contact with THR 103 (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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59A ASP* 3.0 28.9 - - - +
60A GLY* 3.2 26.8 - - - +
84A PRO* 4.0 14.4 - - + -
90B ILE* 4.0 15.3 - - + -
99B LEU* 4.1 13.4 - - + -
100B GLN* 3.1 29.8 + - - +
101B ILE 3.0 0.4 + - - -
102B ARG* 1.3 78.7 - - - +
104B VAL* 1.3 57.6 + - - +
106B LEU* 3.6 0.6 + - - -
107B SER* 3.0 32.2 + - - -
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Residues in contact with VAL 104 (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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67B PRO* 4.6 6.1 - - + -
69B VAL* 4.0 20.6 - - + -
88B LEU* 4.8 0.9 - - + -
90B ILE* 4.0 22.0 - - + +
91B LEU* 4.0 25.6 - - + -
95B TRP* 4.0 26.2 - - + -
100B GLN 4.3 3.1 - - - +
101B ILE* 2.9 10.6 + - + +
103B THR* 1.3 74.5 - - - +
105B LEU* 1.3 69.9 + - + +
107B SER* 3.1 3.2 + - - -
108B ILE* 2.9 46.1 + - + +
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Residues in contact with LEU 105 (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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15B LEU* 3.3 34.8 - - + -
20B VAL* 5.3 2.5 - - + -
23B ILE* 3.9 25.8 - - + +
37B VAL* 4.6 19.5 - - + -
39B ILE* 4.9 10.3 - - + +
54B LEU* 5.0 3.8 - - + -
56B LEU* 4.9 4.9 - - + -
69B VAL* 5.1 7.4 - - + -
101B ILE* 2.9 32.2 + - + +
102B ARG* 3.8 4.7 - - - +
104B VAL* 1.3 80.3 - - + +
106B LEU* 1.3 65.0 + - - +
108B ILE* 3.2 15.8 + - + +
109B GLN* 3.1 21.0 + - - +
201B IOD 4.3 7.0 - - + -
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Residues in contact with LEU 106 (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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58A GLY 4.1 15.5 - - - +
59A ASP* 3.6 31.6 - - - +
20B VAL* 3.7 32.3 - - + -
102B ARG* 2.7 44.0 + - + +
103B THR 3.7 3.8 - - - +
105B LEU* 1.3 74.3 - - - +
107B SER* 1.3 56.7 + - - +
109B GLN* 3.2 16.9 + - - +
110B ALA* 2.9 30.7 + - - +
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Residues in contact with SER 107 (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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59A ASP* 4.5 6.6 + - - -
84A PRO* 5.5 2.9 - - - +
88B LEU* 3.3 26.6 - - - +
90B ILE* 3.4 14.2 - - - +
103B THR* 3.0 21.0 + - - +
104B VAL 3.1 5.8 + - - -
106B LEU* 1.3 78.1 - - - +
108B ILE* 1.3 61.2 + - - +
110B ALA* 3.3 8.7 + - - +
111B LEU* 3.0 24.4 + - - +
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Residues in contact with ILE 108 (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 ILE* 3.9 21.5 - - + -
54B LEU* 4.0 9.0 - - + -
69B VAL* 3.6 31.0 - - + -
71B PHE* 4.1 20.9 - - + -
86B ILE* 3.7 17.0 - - + -
88B LEU* 3.9 14.8 - - + -
91B LEU* 4.9 1.3 - - + -
104B VAL* 2.9 32.7 + - + +
105B LEU* 3.2 11.2 + - + +
107B SER* 1.3 72.1 - - - +
109B GLN* 1.3 67.7 + - - +
111B LEU* 3.0 25.0 + - + +
112B LEU* 3.2 10.3 + - + +
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Residues in contact with GLN 109 (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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20B VAL* 3.7 22.6 - - - +
21B PRO 3.3 18.8 + - - +
22B GLY* 4.0 6.8 - - - +
23B ILE* 4.0 13.6 - - + +
39B ILE* 4.2 15.9 - - + +
40B ALA 5.0 3.3 - - - +
42B PRO* 4.0 11.3 - - + +
105B LEU 3.1 9.3 + - - +
106B LEU* 3.7 18.4 + - - +
108B ILE* 1.3 79.8 - - - +
110B ALA* 1.3 62.4 + - - +
112B LEU* 3.4 21.2 + - + +
113B SER* 3.4 15.3 + - - +
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Residues in contact with ALA 110 (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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106B LEU 2.9 14.3 + - - +
107B SER* 3.4 13.0 - - - +
108B ILE 3.1 0.2 - - - -
109B GLN* 1.3 77.0 - - + +
111B LEU* 1.3 64.3 + - - +
113B SER* 3.1 10.9 + - - -
114B ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 111 (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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77B HIS* 3.0 22.5 + - + +
79B ASN* 3.6 33.4 - - + +
80B VAL* 6.4 0.2 - - + -
86B ILE* 4.3 19.3 - - + -
87B CYS 4.6 6.1 - - - +
88B LEU* 4.2 22.2 - - + -
107B SER 3.0 13.0 + - - +
108B ILE* 3.0 15.5 + - + +
110B ALA* 1.3 77.7 - - - +
112B LEU* 1.3 60.1 + - + +
114B ALA 4.1 6.3 - - - +
115B PRO 3.1 14.7 - - - -
116B ASN* 4.1 19.3 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ILE* 4.3 24.2 - - + -
41B GLY* 4.7 6.7 - - - -
42B PRO* 3.8 22.9 - - + -
45B SER* 4.1 3.7 - - - -
46B PRO* 4.7 1.2 - - - +
47B PHE* 3.3 28.0 - - + -
52B PHE* 5.0 9.2 - - + -
71B PHE* 3.9 31.9 - - + -
75B ILE* 4.2 13.9 - - + -
77B HIS* 3.8 17.9 - - + +
80B VAL* 5.8 1.1 - - + -
108B ILE* 3.5 14.6 - - + +
109B GLN* 3.7 9.4 - - - +
110B ALA 3.1 0.8 - - - -
111B LEU* 1.3 79.3 - - + +
113B SER* 1.3 62.7 + - - +
114B ALA 3.1 0.9 + - - -
115B PRO* 3.8 5.2 - - - +
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Residues in contact with SER 113 (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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42B PRO* 3.2 26.4 - - - +
43B GLN 5.7 1.3 - - - -
44B ASP 5.1 3.5 - - - +
45B SER* 4.2 16.3 - - - -
46B PRO* 6.1 0.2 - - - -
109B GLN* 3.4 7.3 + - - +
110B ALA* 3.1 11.9 + - - -
112B LEU* 1.3 78.4 - - - +
114B ALA* 1.3 62.7 + - - +
115B PRO* 4.1 1.5 - - - +
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Residues in contact with ALA 114 (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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110B ALA 3.0 12.8 + - - +
111B LEU* 3.3 11.7 - - - +
112B LEU 3.1 1.4 - - - -
113B SER* 1.3 83.0 - - - +
115B PRO* 1.4 72.5 - - - +
116B ASN* 4.6 0.5 - - - +
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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