Contacts of the helix formed by residues 77 - 88 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MET* 5.0 0.2 - - - -
76A HIS* 1.3 81.1 - - - +
78A ASP* 1.3 66.6 + - - -
79A SER* 3.3 3.4 - - - -
80A SER* 3.7 14.9 + - - -
81A ILE* 3.3 22.3 + - - +
117B ARG* 4.3 19.6 - - - +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.9 11.3 - - + +
70A MET* 3.4 30.0 - - + +
76A HIS 3.6 1.4 + - - -
77A GLY* 1.3 71.2 - - - -
79A SER* 1.3 83.4 + - - +
81A ILE* 2.9 5.1 + - - +
82A TYR* 2.8 25.1 + - - +
116A MET* 4.7 15.7 - - + -
116B MET* 3.6 23.8 - - - +
117B ARG* 4.7 12.3 - - - +
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 3.3 2.1 - - - -
78A ASP* 1.3 86.5 + - - +
80A SER* 1.3 70.0 + - - +
82A TYR* 4.6 5.6 - - - +
83A ASP* 2.8 41.4 + - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.7 3.6 - - - +
74A HIS* 5.7 2.9 - - - -
76A HIS* 4.9 5.6 - - - +
77A GLY* 3.8 22.9 + - - -
78A ASP 3.2 0.4 - - - -
79A SER* 1.3 82.3 + - - +
81A ILE* 1.3 64.0 + - - +
83A ASP* 3.9 4.0 - - - +
84A ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.1 9.2 - - + -
44A ILE* 3.5 10.7 - - + +
66A VAL* 3.5 17.7 - - + +
69A ILE* 3.8 37.2 - - + -
70A MET* 3.5 33.0 - - + +
74A HIS* 3.4 35.2 - - + +
76A HIS 4.6 0.2 - - - +
77A GLY 3.3 10.3 + - - +
78A ASP 2.9 7.5 + - - +
80A SER* 1.3 73.4 - - - +
82A TYR* 1.3 61.7 + - - +
84A ALA* 3.1 5.7 + - - +
85A MET* 2.8 24.1 + - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A SER* 3.6 17.0 - - - -
66A VAL* 4.1 16.4 - - + -
78A ASP 2.8 18.0 + - - +
79A SER* 4.2 3.4 - - - +
81A ILE* 1.3 73.3 - - - +
83A ASP* 1.3 72.6 + - - +
85A MET* 3.4 11.2 - - - +
86A VAL* 2.8 55.3 + - + +
101A MET* 4.0 4.6 - - + -
104A ASN 5.2 0.2 + - - -
113A PRO* 5.1 5.0 - - + +
114A ALA 2.8 25.8 + - - -
115A ALA* 4.9 0.7 - - - -
116A MET* 3.4 39.8 - - + -
119A THR* 2.8 29.9 + - - +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 2.8 33.0 + - - +
80A SER* 3.9 4.4 - - - +
82A TYR* 1.3 89.4 - - - +
84A ALA* 1.3 62.4 + - - +
86A VAL* 3.3 7.4 + - - +
87A ARG* 3.0 21.1 + - - +
113A PRO* 5.4 8.1 - - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.2 21.3 - - + -
41A GLN* 5.6 6.0 + - + +
44A ILE* 4.6 2.5 - - + -
80A SER 3.2 12.8 + - - +
81A ILE 3.1 10.2 + - - +
83A ASP* 1.3 78.5 - - - +
85A MET* 1.3 65.6 + - - +
87A ARG* 3.2 17.1 + - - +
88A MET* 3.3 21.0 + - + +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.6 21.2 - - + +
48A MET* 4.5 13.5 - - - +
62A SER* 4.7 4.7 - - - -
65A SER* 4.6 15.9 - - - -
66A VAL* 4.9 5.6 - - - -
69A ILE* 5.7 2.7 - - - -
81A ILE* 2.8 13.4 + - + +
82A TYR* 3.2 22.9 + - - +
84A ALA* 1.3 74.9 - - - +
86A VAL* 1.3 64.0 + - - +
88A MET* 3.1 30.0 + - + +
89A SER 3.5 4.2 + - - -
99A VAL* 4.3 12.0 - - + +
101A MET* 4.0 18.7 - - + +
121A ALA* 4.5 14.4 - - - -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 2.8 54.7 + - + +
83A ASP* 3.4 8.1 - - - +
85A MET* 1.3 73.2 - - - +
87A ARG* 1.3 65.4 + - - +
89A SER* 2.5 30.3 + - - +
90A GLN* 3.5 24.5 - - - +
101A MET* 3.5 15.0 - - + -
105A ASN* 4.1 7.2 - - + +
113A PRO* 4.0 24.9 - - + -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 6.1 2.9 - - - +
41A GLN* 5.7 6.6 - - - +
83A ASP 3.0 12.7 + - - +
84A ALA* 3.2 12.0 + - - +
86A VAL* 1.3 76.3 - - - +
88A MET* 1.3 59.1 + - + +
90A GLN* 3.0 35.6 + - - +
93A LYS* 3.9 31.4 + - + +
94A ASN* 2.9 35.1 + - - +
165A ASN 5.6 1.6 + - - -
167A SER* 5.9 4.2 - - - +
168A THR* 4.8 18.5 + - - +
261A TYR* 4.3 16.6 + - - -
262A GLU* 4.8 9.5 + - - +
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.4 41.1 - - + +
44A ILE* 3.5 50.9 - - + -
45A LEU* 4.5 12.1 - - + +
84A ALA 3.3 10.1 - - - +
85A MET* 3.3 17.3 - - - +
86A VAL 3.1 0.6 - - - -
87A ARG* 1.3 77.4 - - + +
89A SER* 1.3 54.4 + - - +
90A GLN 3.4 1.6 - - - -
94A ASN* 3.7 11.5 - - - +
97A ILE* 3.7 5.7 - - - +
98A LEU* 3.2 24.4 + - + +
99A VAL* 3.2 36.1 + - + +
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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