Contacts of the helix formed by residues 101 - 116 (chain B) in PDB entry 3QS7
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 ILE 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.5 1.8 - - + -
22B LEU* 5.7 0.2 - - + -
26B LEU* 3.8 39.3 - - + -
27B LEU 3.7 23.1 - - - +
28B GLN* 3.7 7.2 - - - +
30B TYR* 2.9 28.9 + - + +
32B VAL* 3.6 24.7 - - + +
57B MET* 6.1 0.2 - - + -
60B LEU* 3.3 32.8 - - + -
72B LEU* 5.3 0.9 - - + -
100B ASN* 1.3 71.8 - - - +
102B SER* 1.3 58.8 + - - +
104B LEU* 3.4 4.4 + - + +
105B LEU* 2.9 38.2 + - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 6.5 0.2 - - - -
28B GLN* 3.4 46.4 + - - +
100B ASN* 3.6 10.4 + - - +
101B ILE* 1.3 84.4 - - - +
103B ARG* 1.4 58.4 + - - +
105B LEU* 3.6 6.5 + - - +
106B GLN* 3.1 29.6 + - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 5.3 7.5 - - - +
97B VAL* 6.2 0.2 - - - +
99B THR* 3.1 30.9 + - - +
100B ASN* 2.8 16.2 + - + +
102B SER* 1.4 79.5 + - - +
104B LEU* 1.3 59.1 + - - +
106B GLN* 3.3 5.8 + - - +
107B GLU* 3.0 34.8 + - - +
-2C SER 4.4 13.7 + - - +
-1C HIS* 3.6 8.9 + - - +
0C MET* 3.6 38.2 - - - +
83C THR* 3.3 29.9 + - - -
84C LYS* 5.1 0.4 - - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.7 34.1 - - + -
33B THR 4.1 5.6 - - - +
34B VAL* 3.9 26.7 - - + -
49B ARG 5.5 0.7 - - - +
52B LEU 5.7 0.2 - - - -
53B ALA* 4.0 26.2 - - + +
56B TRP* 3.9 29.2 - - + -
57B MET* 5.0 9.4 - - + -
60B LEU* 5.7 1.1 - - + -
99B THR* 4.9 1.0 - - + +
100B ASN 3.1 4.8 + - - -
101B ILE* 3.4 12.3 + - + +
103B ARG* 1.3 77.5 - - - +
105B LEU* 1.3 58.9 + - + +
107B GLU* 3.4 6.7 + - + +
108B THR* 2.9 36.0 + - - +
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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
----------------------------------------------------------
19B ILE* 3.8 33.3 - - + +
22B LEU* 3.4 32.1 - - + -
23B SER* 4.3 9.6 - - - +
26B LEU* 3.6 18.4 - - + -
28B GLN* 5.8 0.2 - - - +
57B MET* 3.4 33.2 - - + -
75B VAL* 4.9 1.8 - - + -
101B ILE* 2.9 29.0 + - + +
102B SER* 3.9 6.5 - - - +
104B LEU* 1.3 74.1 - - + +
106B GLN* 1.3 64.9 + - - +
108B THR* 3.4 6.8 + - + +
109B SER* 3.1 22.0 + - - -
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.8 0.2 - - - -
102B SER 3.1 18.9 + - - +
103B ARG* 3.7 6.3 - - + +
104B LEU 3.3 0.2 - - - -
105B LEU* 1.3 73.1 - - - +
107B GLU* 1.3 66.2 + - - +
109B SER* 3.3 11.7 + - - -
110B GLU* 3.1 46.1 + - - +
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Residues in contact with GLU 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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34B VAL* 6.0 4.0 - - + -
49B ARG* 5.9 0.4 - - - +
103B ARG* 3.0 22.2 + - - +
104B LEU* 3.7 7.6 - - + +
106B GLN* 1.3 74.2 - - - +
108B THR* 1.3 55.9 + - - +
110B GLU* 3.0 15.0 + - - +
111B GLN* 2.8 55.0 + - - +
-2C SER 4.4 14.4 - - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.4 9.6 - - + -
50B LEU* 3.9 15.9 - - + +
53B ALA* 3.3 24.9 - - - +
57B MET* 5.2 3.5 - - + +
75B VAL* 5.4 6.5 - - + -
79B ILE* 4.0 22.2 - - + -
104B LEU* 2.9 22.2 + - - +
105B LEU* 3.6 9.6 - - + -
106B GLN 3.3 0.2 - - - -
107B GLU* 1.3 75.7 - - - +
109B SER* 1.3 62.2 + - - +
111B GLN* 3.3 12.3 + - - +
112B LEU* 3.0 28.7 + - + +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.6 17.7 - - - -
16B ALA* 4.3 10.4 - - - +
19B ILE* 4.0 21.1 - - - +
105B LEU 3.1 14.0 + - - -
106B GLN* 3.4 17.7 - - - -
107B GLU 3.2 0.2 - - - -
108B THR* 1.3 75.4 - - - +
110B GLU* 1.3 62.7 + - - +
112B LEU* 3.1 5.7 + - - +
113B VAL* 3.1 28.4 + - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 3.1 39.5 + - - +
107B GLU* 3.0 12.9 + - - +
109B SER* 1.3 75.5 - - - +
111B GLN* 1.3 57.9 + - + +
113B VAL* 3.2 9.8 + - - +
114B ALA* 3.0 28.8 + - - +
-2C SER* 3.6 38.6 + - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY* 4.0 20.7 - - - +
49B ARG* 3.1 44.7 + - - +
50B LEU* 3.4 37.6 + - + +
53B ALA* 4.8 0.2 - - - +
107B GLU* 2.8 37.4 + - - +
108B THR* 3.4 13.2 + - - +
109B SER 3.3 0.2 - - - -
110B GLU* 1.3 69.6 - - + +
112B LEU* 1.3 60.7 + - - +
114B ALA* 3.6 5.6 + - - +
115B LEU* 3.0 31.9 + - - +
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Residues in contact with LEU 112 (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 ILE* 3.8 32.1 - - + +
15B PHE* 3.4 44.0 - - + -
19B ILE* 4.5 4.7 - - + -
50B LEU* 4.0 14.8 - - + -
78B GLU* 4.1 10.5 - - + +
79B ILE* 3.7 32.3 - - + -
81B PHE* 4.2 2.9 - - + -
108B THR* 3.0 21.7 + - + +
109B SER 3.1 7.4 + - - +
111B GLN* 1.3 72.3 - - - +
113B VAL* 1.3 60.7 - - - +
115B LEU* 3.4 2.8 + - - +
116B LYS* 2.9 31.9 + - - +
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Residues in contact with VAL 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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15B PHE* 3.5 20.4 - - + -
16B ALA* 6.4 0.2 - - + -
109B SER* 3.1 19.5 + - - +
110B GLU* 3.2 11.4 + - - +
112B LEU* 1.3 76.9 - - - +
114B ALA* 1.3 62.7 + - + +
116B LYS* 3.4 6.6 + - - +
117B PRO* 3.3 17.8 - - - +
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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 GLU 3.0 15.4 + - - +
111B GLN* 4.1 6.1 - - - +
113B VAL* 1.3 78.6 - - + +
115B LEU* 1.3 57.4 + - - +
117B PRO* 3.3 14.7 - - - +
118B TRP* 3.5 15.2 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.9 13.9 - - + -
43B LEU 4.9 7.4 - - - +
46B GLY* 4.7 2.9 - - - -
47B LEU* 3.8 31.4 - - + +
50B LEU* 3.5 30.3 - - + -
81B PHE* 4.8 1.8 - - + -
111B GLN 3.0 16.6 + - - +
112B LEU* 3.8 3.4 - - - +
114B ALA* 1.3 77.1 - - - +
116B LYS* 1.3 60.6 + - - +
117B PRO* 3.4 0.7 - - - -
118B TRP* 3.1 8.6 + - + +
119B ILE* 2.9 38.2 + - + +
124B PHE* 4.4 27.1 - - + -
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Residues in contact with LYS 116 (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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9B SER* 5.7 1.9 - - - -
11B ILE* 3.8 23.3 - - + +
15B PHE* 5.5 2.9 - - + -
112B LEU 2.9 18.2 + - - +
113B VAL* 3.5 8.1 - - - +
115B LEU* 1.3 76.3 - - - +
117B PRO* 1.4 65.9 - - + +
118B TRP 3.3 0.9 + - - -
119B ILE* 3.7 13.7 - - - +
120B THR* 5.7 0.3 + - - -
121B ARG* 5.3 0.3 + - - -
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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
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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