Contacts of the helix formed by residues 76 - 87 (chain B) in PDB entry 1KPH
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B CYS 3.0 16.6 + - - -
74B GLY 3.2 2.6 + - - -
75B TRP* 1.3 78.0 - - - +
77B ALA* 1.3 62.9 + - - +
78B THR 3.3 3.4 - - - -
79B MET* 3.4 15.3 + - - +
80B MET* 3.1 30.0 + - - +
103B VAL* 3.6 12.5 - - - +
106B LEU* 4.6 4.5 - - - -
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Residues in contact with ALA 77 (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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30B THR* 3.5 35.4 + - + +
32B THR* 3.6 21.1 - - - +
50B ILE* 5.9 0.7 - - + -
53B ILE* 4.0 8.6 - - + +
73B CYS 4.7 0.8 + - - -
75B TRP 3.6 4.4 + - - -
76B GLY* 1.3 75.8 - - - +
78B THR* 1.3 57.7 + - - +
80B MET* 3.6 4.9 + - - +
81B ARG* 3.0 29.8 + - - +
106B LEU* 5.9 0.7 - - - -
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 5.9 1.2 - - - +
52B LYS* 5.5 0.9 - - - -
53B ILE* 3.8 29.5 - - + +
57B LEU* 4.1 24.4 - - + +
68B LEU* 5.4 1.1 - - + -
70B ASP* 3.5 21.3 - - + +
73B CYS 5.4 2.4 + - - -
76B GLY* 3.3 0.8 - - - -
77B ALA* 1.3 76.2 - - - +
79B MET* 1.3 64.8 + - - +
81B ARG* 3.3 2.6 + - - +
82B ALA* 2.9 22.5 + - - +
134B VAL* 4.3 11.0 - - + -
136B ILE* 4.1 20.1 - - + +
2900B SAH 5.1 10.5 + - - -
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Residues in contact with MET 79 (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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68B LEU* 5.7 1.3 - - - -
70B ASP* 4.0 24.6 + - + +
73B CYS* 3.6 28.7 - - + -
76B GLY* 3.4 7.9 + - - +
78B THR* 1.3 78.6 - - - +
80B MET* 1.3 80.7 + - + +
82B ALA* 3.1 9.1 + - - +
83B VAL* 3.0 30.8 + - - +
90B VAL* 3.6 23.0 - - + +
91B VAL 4.9 0.2 - - - -
92B GLY* 3.6 11.0 - - - +
103B VAL* 4.0 21.3 - - + -
107B VAL* 5.1 1.3 - - + -
117B ARG 3.3 29.8 - - - +
118B VAL* 4.5 0.4 - - + -
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Residues in contact with MET 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 3.1 17.1 + - - +
77B ALA* 4.0 4.3 - - - +
79B MET* 1.3 124.7 - - + +
81B ARG* 1.3 60.0 - - - +
83B VAL* 3.3 4.9 + - + +
84B GLU* 2.9 51.8 + - - +
90B VAL* 4.4 6.7 - - + -
103B VAL* 4.7 5.4 - - + -
106B LEU* 4.1 35.9 - - + +
107B VAL* 4.7 8.5 - - + -
110B SER* 5.6 2.7 - - - -
116B LYS* 4.4 21.3 - - + -
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Residues in contact with ARG 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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50B ILE* 3.5 33.7 - - + +
53B ILE* 3.6 26.5 - - + -
54B ASP* 2.8 38.2 + - - +
57B LEU* 4.2 4.3 - - + -
77B ALA 3.0 19.5 + - - +
78B THR 3.6 4.5 - - - +
80B MET* 1.3 75.8 - - - +
82B ALA* 1.3 56.8 + - - +
84B GLU* 4.7 4.3 - - - -
85B LYS* 2.7 74.3 + - - +
86B TYR* 3.8 1.9 + - + -
129C PRO* 5.2 1.0 - - - +
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Residues in contact with ALA 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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57B LEU* 3.8 14.6 - - + +
62B LEU* 5.2 1.3 - - + -
68B LEU* 3.6 30.3 - - + -
78B THR 2.9 14.8 + - - +
79B MET* 3.3 10.5 - - - +
81B ARG* 1.3 77.2 - - - +
83B VAL* 1.3 60.8 + - - +
86B TYR* 3.1 25.0 + - - +
87B ASP 3.2 6.9 + - - -
88B VAL* 3.5 14.7 + - + +
90B VAL* 3.9 3.1 - - + -
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Residues in contact with VAL 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 MET 3.0 17.7 + - - +
80B MET* 3.6 9.6 - - + +
82B ALA* 1.3 76.5 - - - +
84B GLU* 1.3 63.1 + - + +
87B ASP* 3.1 26.5 + - - +
88B VAL 3.5 19.5 - - - +
90B VAL* 3.5 24.2 - - + +
112B ASN* 3.2 41.4 - - + +
114B ARG* 4.2 4.0 - - + -
115B SER 4.8 0.4 - - - +
116B LYS* 3.7 28.3 - - + -
156C ARG* 4.9 0.3 - - - -
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 2.9 40.5 + - - +
81B ARG* 4.3 4.0 + - - +
83B VAL* 1.3 82.3 - - + +
85B LYS* 1.3 59.2 + - + +
110B SER* 5.0 7.6 + - - -
111B GLU* 5.1 9.7 - - - +
112B ASN* 4.4 14.2 - - + +
156C ARG* 3.1 23.6 - - - +
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Residues in contact with LYS 85 (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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81B ARG* 2.7 56.1 + - - +
84B GLU* 1.3 75.6 - - + +
86B TYR* 1.3 76.7 + - + +
87B ASP 3.6 0.2 - - - -
127C ASP* 4.0 1.2 - - - +
129C PRO* 3.6 32.2 - - + +
156C ARG* 2.9 46.6 + - - +
157C LEU* 3.2 17.2 + - - +
158C LEU 3.1 20.4 + - - -
159C PRO* 4.4 4.4 - - - +
287C LYS* 4.9 0.8 - - - +
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Residues in contact with TYR 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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54B ASP* 2.8 45.5 + - - +
57B LEU* 3.7 37.0 - - + -
58B GLY* 4.5 5.2 + - - -
62B LEU* 3.9 26.0 - - + -
64B PRO 4.3 1.0 - - - -
81B ARG* 3.8 9.0 - - + -
82B ALA* 3.1 9.4 + - - +
85B LYS* 1.3 92.9 - - + +
87B ASP* 1.3 70.8 + - - +
88B VAL* 3.4 7.0 + - + +
127C ASP* 2.6 48.7 - - - +
129C PRO* 3.8 30.3 - - + +
156C ARG* 3.5 3.4 - - - -
157C LEU* 6.2 0.2 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.3 13.0 - - + +
65B GLY 3.2 17.7 + - - -
82B ALA 3.2 0.4 + - - -
83B VAL 3.1 18.6 + - - +
85B LYS 3.6 1.4 - - - -
86B TYR* 1.3 80.9 - - - +
88B VAL* 1.3 57.8 + - - +
112B ASN* 4.5 5.0 + - - +
114B ARG* 2.9 46.9 + - - +
156C ARG* 3.5 29.2 + - - +
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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