Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 3KSA
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 GLY 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ARG* 4.3 20.2 - - - +
70B MET* 4.3 0.4 - - - -
76B HIS* 1.3 81.1 - - - +
78B ASP* 1.3 66.8 + - - -
79B SER* 3.3 3.4 - - - -
80B SER* 3.7 15.4 + - - -
81B ILE* 3.3 22.5 + - - +
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Residues in contact with ASP 78 (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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116A MET* 3.6 23.6 - - - +
117A ARG* 4.7 13.7 - - - +
66B VAL* 3.9 9.8 - - + +
70B MET* 3.4 30.9 - - + +
76B HIS 3.6 1.8 + - - -
77B GLY* 1.3 70.2 - - - -
79B SER* 1.3 83.2 + - - +
81B ILE* 3.0 5.2 + - - +
82B TYR* 2.8 25.3 + - - +
116B MET* 4.7 14.8 - - + -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY* 3.3 1.6 - - - -
78B ASP* 1.3 86.5 + - - +
80B SER* 1.3 70.5 + - - +
82B TYR* 4.6 6.3 - - - +
83B ASP* 2.8 41.2 + - - +
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Residues in contact with SER 80 (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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40B VAL* 4.7 3.4 - - - +
74B HIS* 5.7 3.1 - - - -
76B HIS* 4.9 6.3 - - - +
77B GLY* 3.8 22.4 + - - -
78B ASP 3.2 0.4 - - - -
79B SER* 1.3 85.5 + - - +
81B ILE* 1.3 63.1 + - - +
83B ASP* 3.9 4.1 - - - +
84B ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 81 (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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40B VAL* 4.1 9.0 - - + -
44B ILE* 3.5 11.6 - - + +
66B VAL* 3.6 18.8 - - + +
69B ILE* 3.8 37.7 - - + -
70B MET* 3.6 32.5 - - + +
74B HIS* 3.4 34.8 - - + +
76B HIS 4.6 0.2 - - - +
77B GLY 3.3 10.5 - - - +
78B ASP 3.0 7.5 + - - +
80B SER* 1.3 75.2 - - - +
82B TYR* 1.3 61.8 + - - +
84B ALA* 3.1 5.9 + - - +
85B MET* 2.8 24.1 + - + -
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Residues in contact with TYR 82 (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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62B SER* 3.6 16.4 - - - -
66B VAL* 4.1 17.7 - - + -
78B ASP 2.8 17.8 + - - +
79B SER* 4.2 3.8 - - - +
81B ILE* 1.3 73.6 - - - +
83B ASP* 1.3 72.5 + - - +
85B MET* 4.0 11.7 - - - -
86B VAL* 2.8 51.6 + - + +
101B MET* 4.0 5.0 - - + -
104B ASN 5.2 0.2 + - - -
105B ASN* 6.1 0.2 - - - -
113B PRO* 5.1 5.0 - - + +
114B ALA 2.8 25.5 + - - -
115B ALA* 4.9 0.9 - - - -
116B MET* 3.4 38.0 - - + -
119B THR* 2.7 31.0 + - - +
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Residues in contact with ASP 83 (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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79B SER* 2.8 33.2 + - - +
80B SER* 3.9 4.9 - - - +
82B TYR* 1.3 88.5 - - - +
84B ALA* 1.3 56.9 + - - +
86B VAL* 3.3 8.1 + - - +
87B ARG* 3.0 25.3 + - - +
113B PRO* 5.3 8.7 - - - +
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Residues in contact with ALA 84 (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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40B VAL* 4.2 21.5 - - + -
41B GLN* 5.5 6.4 + - + +
44B ILE* 4.6 2.0 - - + -
80B SER 3.2 12.5 + - - +
81B ILE 3.1 10.4 + - - +
83B ASP* 1.3 76.6 - - - +
85B MET* 1.3 63.9 + - - +
87B ARG* 3.2 16.6 + - - +
88B MET* 3.3 20.9 + - + +
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.6 21.3 - - + +
48B MET* 4.5 13.0 - - - +
62B SER* 4.7 4.7 - - - -
65B SER* 4.6 16.2 - - - -
66B VAL* 5.0 5.6 - - - -
69B ILE* 5.7 2.2 - - - -
81B ILE* 2.8 13.6 + - + +
82B TYR* 3.2 22.9 + - - +
84B ALA* 1.3 74.7 - - - +
86B VAL* 1.3 63.5 + - - +
88B MET* 3.1 29.9 + - - +
89B SER 3.6 4.0 + - - -
99B VAL* 4.3 11.5 - - + +
101B MET* 3.9 15.0 - - + +
121B ALA* 4.5 18.8 - - - -
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Residues in contact with VAL 86 (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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82B TYR* 2.8 56.2 + - + +
83B ASP* 3.4 8.5 - - - +
84B ALA 3.2 0.2 - - - -
85B MET* 1.3 73.2 - - - +
87B ARG* 1.3 66.9 + - - +
89B SER* 2.5 30.9 + - - +
90B GLN* 3.5 24.1 - - - +
101B MET* 3.5 14.8 - - + -
105B ASN* 4.2 7.9 - - + +
113B PRO* 4.0 25.6 - - + -
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Residues in contact with ARG 87 (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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38B LYS* 6.1 2.9 - - - +
41B GLN* 5.7 6.8 - - - +
83B ASP 3.0 13.2 + - - +
84B ALA* 3.2 12.3 + - - +
86B VAL* 1.3 74.7 - - - +
88B MET* 1.3 59.8 + - + +
90B GLN* 3.0 35.6 + - - +
93B LYS* 3.9 32.6 + - + +
94B ASN* 2.9 36.7 + - - +
165B ASN 5.6 1.2 + - - -
167B SER* 5.9 3.6 - - - +
168B THR* 4.8 18.6 + - - +
261B TYR* 4.3 16.6 + - - -
262B GLU* 4.9 9.5 + - - +
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 3.4 40.6 - - + +
44B ILE* 3.6 50.7 - - + -
45B LEU* 4.6 11.7 - - + +
84B ALA 3.3 10.5 - - - +
85B MET* 3.3 17.3 - - - +
86B VAL 3.1 0.8 - - - -
87B ARG* 1.3 77.6 - - + +
89B SER* 1.3 54.1 + - - +
90B GLN 3.4 1.6 - - - -
94B ASN* 3.7 11.1 - - - +
97B ILE* 3.7 5.9 - - - +
98B LEU* 3.2 25.8 + - + +
99B VAL* 3.2 36.4 + - + +
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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