Contacts of the helix formed by residues 77 - 94 (chain A) in PDB entry 1K1S
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 ARG 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 3.1 33.7 + - - +
19A LEU* 3.4 28.5 - - - +
20A ASN* 4.9 2.8 + - - +
75A PRO* 3.8 14.1 + - + +
76A MET* 1.3 77.3 - - - +
78A LYS* 1.3 64.7 + - - +
79A PRO* 3.3 8.3 - - + -
80A ILE* 3.1 41.9 + - + +
81A TYR* 3.5 16.4 + - - -
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Residues in contact with LYS 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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12A PHE* 5.0 5.2 - - + -
76A MET* 3.6 30.4 + - + -
77A ARG* 1.3 74.4 - - - +
79A PRO* 1.3 64.6 - - + +
81A TYR* 3.0 18.0 + - + +
82A GLU* 2.8 61.6 + - + +
104A ILE* 4.7 14.1 - - + -
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Residues in contact with PRO 79 (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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77A ARG* 3.3 8.7 - - + -
78A LYS* 1.3 94.8 - - + +
80A ILE* 1.3 58.2 + - + +
82A GLU* 3.7 15.6 - - + +
83A ALA* 3.1 25.5 + - - +
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Residues in contact with ILE 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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15A VAL* 4.0 7.2 - - + -
16A GLU* 5.1 0.7 - - - +
19A LEU* 3.8 17.3 - - + -
77A ARG* 3.2 63.0 - - + +
78A LYS 3.0 0.8 - - - -
79A PRO* 1.3 78.4 - - + +
81A TYR* 1.3 66.7 + - + +
83A ALA* 3.2 6.2 + - + +
84A PHE* 3.1 51.4 + - + -
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Residues in contact with TYR 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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11A PHE* 3.4 13.4 - - + -
12A PHE* 3.4 69.1 - + + -
15A VAL* 4.1 23.6 - - + -
16A GLU* 3.0 28.3 + - + +
30A VAL* 3.6 16.6 - - - +
75A PRO 4.1 0.3 + - - -
76A MET* 3.4 25.3 - - + -
77A ARG 3.5 20.1 + - - -
78A LYS* 3.0 17.2 + - - +
80A ILE* 1.3 76.5 - - + +
82A GLU* 1.3 61.7 + - - +
84A PHE* 3.3 3.5 + - - -
85A SER* 2.8 30.3 + - - -
104A ILE* 4.0 3.1 - - + -
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Residues in contact with GLU 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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78A LYS* 2.8 57.3 + - + +
79A PRO* 3.7 15.2 - - - +
81A TYR* 1.3 76.7 - - - +
83A ALA* 1.3 61.6 + - - +
85A SER* 3.2 7.7 + - - -
86A ASN* 2.8 37.8 + - - +
104A ILE* 4.2 7.2 - - + -
246A HIS* 5.4 7.6 - - - -
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Residues in contact with ALA 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 PRO 3.1 13.2 + - - +
80A ILE* 3.3 11.7 - - - +
82A GLU* 1.3 80.3 - - - +
84A PHE* 1.3 64.0 + - + +
86A ASN* 3.2 10.2 + - - +
87A ARG* 3.1 44.7 + - - +
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Residues in contact with PHE 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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11A PHE* 3.7 15.0 - - + -
15A VAL* 3.8 19.3 - - + -
18A VAL* 4.6 11.7 - - + -
19A LEU* 4.5 16.6 - - + -
80A ILE* 3.1 42.5 + - + +
81A TYR 3.6 7.0 - - - +
83A ALA* 1.3 79.8 - - + +
85A SER* 1.3 63.9 + - - +
87A ARG* 3.2 32.9 + - - +
88A ILE* 3.0 28.4 + - + +
137A GLU* 4.2 22.2 - - + -
139A ILE* 3.4 28.7 - - + -
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Residues in contact with SER 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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8A PHE* 4.3 6.1 - - - -
11A PHE* 3.7 6.9 - - - -
81A TYR 2.8 20.2 + - - -
82A GLU* 3.4 6.3 - - - -
84A PHE* 1.3 74.5 - - - +
86A ASN* 1.3 58.4 + - - +
88A ILE* 3.3 1.9 + - - +
89A MET* 2.9 44.7 + - - +
104A ILE* 2.8 44.6 + - - +
244A ILE* 4.9 4.9 - - - +
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Residues in contact with ASN 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 GLU* 2.8 33.0 + - - +
83A ALA* 3.6 9.4 - - - +
85A SER* 1.3 76.0 - - - +
87A ARG* 1.3 63.9 + - - +
89A MET* 4.6 4.3 - - - -
90A ASN* 3.1 40.3 + - - +
244A ILE* 6.1 0.7 - - - +
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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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83A ALA* 3.1 28.5 + - - +
84A PHE* 3.2 53.2 + - - +
86A ASN* 1.3 80.2 - - - +
88A ILE* 1.3 61.1 + - - +
90A ASN* 4.2 4.3 - - - +
91A LEU* 3.3 22.0 + - - +
137A GLU* 3.4 32.5 + - - +
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Residues in contact with ILE 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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8A PHE* 3.6 40.2 - - + -
11A PHE* 4.6 1.6 - - + -
84A PHE* 3.0 16.8 + - + +
85A SER 3.9 2.2 - - - +
87A ARG* 1.3 75.1 - - - +
89A MET* 1.3 59.2 - - - +
91A LEU* 2.9 10.4 + - - +
92A LEU* 2.9 30.4 + - + +
133A ILE* 3.7 45.8 - - + -
137A GLU* 3.7 21.5 - - + -
139A ILE* 4.3 25.6 - - + -
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Residues in contact with MET 89 (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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8A PHE* 4.0 14.1 - - + -
85A SER* 2.9 37.0 + - - +
86A ASN* 3.9 5.2 - - - +
88A ILE* 1.3 75.8 - - - +
90A ASN* 1.3 65.4 + - - +
92A LEU* 3.2 23.5 + - - +
93A ASN* 2.9 24.1 + - - +
99A ILE* 3.6 8.7 - - + +
101A VAL* 3.2 46.7 - - + -
103A SER 3.3 15.0 - - - +
104A ILE 4.7 0.4 - - - -
106A GLU 3.5 18.6 - - - +
107A ALA* 3.9 8.5 - - + -
244A ILE* 6.0 1.3 - - + -
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Residues in contact with ASN 90 (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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86A ASN* 3.1 26.2 + - - +
87A ARG* 4.2 4.8 - - - +
89A MET* 1.3 81.2 - - - +
91A LEU* 1.3 64.5 + - - +
92A LEU 3.2 0.2 - - - -
93A ASN* 3.5 22.0 + - - +
94A LYS* 3.8 8.8 + - - +
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Residues in contact with LEU 91 (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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87A ARG 3.3 14.0 + - - +
88A ILE* 2.9 16.1 + - - +
90A ASN* 1.3 79.4 - - - +
92A LEU* 1.3 57.3 + - + +
94A LYS* 3.1 33.0 - - - +
95A HIS* 3.1 23.2 - - + +
132A GLU* 3.1 44.4 - - + +
133A ILE* 4.2 26.9 - - + -
136A LYS* 3.8 21.5 - - + +
137A GLU* 5.0 6.5 - - + +
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Residues in contact with LEU 92 (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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6A VAL* 4.3 21.5 - - + -
8A PHE* 4.7 2.2 - - + -
88A ILE* 2.9 24.0 + - + +
89A MET* 3.4 29.2 - - - +
91A LEU* 1.3 79.0 - - + +
93A ASN* 1.3 63.1 + - - +
94A LYS 3.2 0.7 - - - -
95A HIS* 3.0 22.0 + - + +
96A ALA* 3.7 4.9 + - - +
99A ILE* 3.8 10.1 - - + +
107A ALA* 4.2 15.9 - - + -
109A LEU* 3.9 17.1 - - + +
129A ILE* 3.5 32.3 - - + -
133A ILE* 3.8 15.0 - - + -
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Residues in contact with ASN 93 (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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89A MET 2.9 12.2 + - - +
90A ASN* 3.5 18.5 + - - +
91A LEU 3.4 0.2 - - - -
92A LEU* 1.3 77.7 - - - +
94A LYS* 1.3 63.2 + - - +
96A ALA* 3.4 17.8 + - - +
99A ILE* 3.6 30.6 - - + +
240A ASN* 5.3 2.4 + - - +
343A ILE* 5.4 1.4 - - - +
344A ASN* 5.6 5.5 - - - +
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Residues in contact with LYS 94 (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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90A ASN 3.8 6.2 + - - +
91A LEU* 3.1 40.8 - - - +
93A ASN* 1.3 81.6 - - - +
95A HIS* 1.3 77.4 + - + +
96A ALA 3.4 1.3 + - - -
114A LYS* 4.7 11.4 + - - +
132A GLU* 3.2 20.6 + - - -
136A LYS* 3.5 9.9 - - - +
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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