Contacts of the helix formed by residues 100 - 113 (chain B) in PDB entry 6P7B
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 ASN 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLY* 3.6 28.9 - - - +
98B TYR 3.2 1.0 - - - +
99B ARG* 1.3 85.4 + - - +
101B ARG* 1.3 55.3 + - - +
103B LYS* 4.9 0.2 - - - -
104B GLN* 2.8 49.0 + - + +
10E G 5.7 1.9 + - - +
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Residues in contact with ARG 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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7B ASP* 5.3 0.2 + - - -
60B GLU* 4.0 19.8 + - - -
91B PRO* 6.2 0.8 - - - +
93B PHE* 4.4 31.3 + - + +
96B GLY 3.5 11.9 + - - +
97B SER 3.3 25.6 - - - +
98B TYR* 3.4 6.1 + - - +
100B ASN* 1.3 78.0 - - - +
102B LYS* 1.3 64.3 + - - +
104B GLN* 3.9 1.9 - - - +
105B SER* 2.9 31.5 + - - -
135B ASN* 4.2 15.9 - - - +
24E A 5.5 11.1 + - - -
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Residues in contact with LYS 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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98B TYR 3.5 10.8 + - - +
101B ARG* 1.3 85.0 - - + +
103B LYS* 1.3 60.1 + - + +
105B SER* 3.3 5.9 + - - -
106B ILE* 2.9 45.1 + - + +
129B LYS* 3.9 21.0 - - - +
131B ASP* 3.8 40.2 + - + +
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Residues in contact with LYS 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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99B ARG 3.3 22.2 + - - +
100B ASN* 3.8 1.3 + - - +
101B ARG 3.4 0.2 - - - -
102B LYS* 1.3 81.9 - - + +
104B GLN* 1.3 57.6 + - - +
106B ILE* 3.2 22.2 - - + +
107B ASP* 2.9 63.7 + - - +
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Residues in contact with GLN 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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93B PHE* 3.8 39.2 - - + +
95B GLY* 5.8 2.4 + - - -
96B GLY 5.6 1.7 + - - -
100B ASN* 2.8 31.4 + - + +
101B ARG* 3.9 1.7 - - - +
103B LYS* 1.3 76.6 - - - +
105B SER* 1.3 62.9 + - - +
107B ASP* 3.8 6.6 - - - +
108B VAL* 2.9 28.0 + - + +
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Residues in contact with SER 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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93B PHE* 3.4 19.5 - - - -
101B ARG* 2.9 20.3 + - - -
102B LYS* 3.5 7.6 - - - -
103B LYS 3.2 0.2 - - - -
104B GLN* 1.3 75.8 - - - +
106B ILE* 1.3 59.3 + - - +
108B VAL* 3.1 4.7 - - - +
109B PHE* 2.9 26.5 + - - +
131B ASP* 5.5 2.7 + - - -
134B ALA* 3.6 13.5 - - - +
135B ASN* 3.7 13.6 + - - +
138B ASN* 2.8 23.8 + - - -
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Residues in contact with ILE 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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102B LYS* 2.9 35.9 + - - +
103B LYS* 3.2 43.7 - - + +
105B SER* 1.3 74.9 - - - +
107B ASP* 1.3 59.5 + - - +
109B PHE* 3.4 8.4 - - - +
110B ILE* 2.9 33.1 + - + +
130B LEU* 4.0 17.8 - - + +
131B ASP* 3.9 35.4 - - + +
134B ALA* 4.0 7.9 - - + -
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Residues in contact with ASP 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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103B LYS* 2.9 61.8 + - - +
104B GLN* 3.8 6.8 + - - +
105B SER 3.2 0.2 - - - -
106B ILE* 1.3 76.0 - - - +
108B VAL* 1.3 65.9 + - - +
110B ILE* 3.2 11.3 + - - +
111B GLN* 3.0 25.0 + - - +
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Residues in contact with VAL 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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93B PHE* 3.5 19.3 - - + -
104B GLN* 2.9 18.7 + - + +
105B SER 3.1 15.7 - - - +
107B ASP* 1.3 76.5 - - - +
109B PHE* 1.3 56.6 + - - +
111B GLN* 3.9 5.1 - - + +
112B LYS* 2.9 44.3 + - + +
138B ASN* 3.3 24.2 - - - +
141B LEU* 6.4 0.9 - - + -
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Residues in contact with PHE 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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32B ILE* 3.8 17.5 - - + -
105B SER 2.9 19.0 + - - +
106B ILE 3.4 6.3 - - - +
108B VAL* 1.3 76.7 - - - +
110B ILE* 1.3 67.3 + - + +
111B GLN 3.0 0.3 + - - -
112B LYS 3.2 0.2 + - - -
113B ILE* 3.0 65.3 + - + +
123B ILE* 5.0 9.6 - - + -
124B LEU* 4.0 17.3 - - + -
130B LEU* 4.9 8.1 - - + -
133B ILE* 4.0 26.9 - - + -
134B ALA* 3.5 28.3 - - + -
137B PHE* 3.6 30.3 - + + -
138B ASN* 4.4 5.6 - - - +
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Residues in contact with ILE 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 ILE* 2.9 19.3 + - + +
107B ASP* 3.2 12.5 + - - +
109B PHE* 1.3 75.4 - - + +
111B GLN* 1.3 70.2 + - + +
113B ILE* 3.4 17.6 - - - +
114B SER* 4.4 5.4 + - - -
120B LYS* 4.5 4.2 + - - +
124B LEU* 3.7 40.2 - - + -
130B LEU* 4.8 8.7 - - + -
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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
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107B ASP 3.0 16.7 + - - +
108B VAL* 3.9 6.7 - - + +
110B ILE* 1.3 86.0 - - + +
112B LYS* 1.3 61.7 + - + +
113B ILE 3.5 0.4 + - - -
114B SER* 4.3 10.8 + - - -
115B GLU* 5.5 3.3 - - - +
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Residues in contact with LYS 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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108B VAL* 2.9 27.0 + - + +
109B PHE 3.8 0.2 - - - -
111B GLN* 1.3 76.6 - - + +
113B ILE* 1.3 64.5 + - - +
114B SER 3.3 2.4 + - - -
115B GLU* 2.7 43.8 + - - +
116B TYR* 3.4 32.3 - - + -
137B PHE* 4.1 9.9 - - + -
141B LEU* 3.6 23.8 - - + -
145B GLU* 5.6 3.4 - - - -
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Residues in contact with ILE 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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29B LEU* 6.3 0.4 - - + -
109B PHE* 3.0 64.0 + - + +
110B ILE* 3.4 23.3 - - - +
112B LYS* 1.3 78.8 - - - +
114B SER* 1.3 67.7 + - - +
116B TYR* 3.0 14.4 + - - +
117B THR* 3.1 26.7 - - + +
120B LYS* 3.6 29.8 - - + +
123B ILE* 6.5 0.7 - - + -
124B LEU* 3.8 14.6 - - + -
137B PHE* 4.1 17.7 - - + -
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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