Contacts of the helix formed by residues 80 - 97 (chain B) in PDB entry 4KMR
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 GLN 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 3.9 13.9 - - - +
77B GLU* 3.1 43.9 + - + +
78B LEU 3.1 3.3 - - - +
79B GLY* 1.3 76.5 - - - +
81B ALA* 1.3 67.1 + - - +
82B PHE* 3.3 2.5 - - + +
83B PHE* 3.0 43.7 + - + +
84B ALA 3.0 10.4 + - - -
107B GLY* 5.8 1.2 + - - -
133B LEU* 4.7 7.3 - - - +
230B TRP 5.3 6.5 - - - +
231B ASP* 6.4 2.2 - - + -
256B ASN* 5.7 2.1 + - - -
258B ASP* 4.8 11.8 - - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 5.2 0.2 - - - -
79B GLY 3.7 4.6 + - - -
80B GLN* 1.3 69.0 - - - +
82B PHE* 1.3 63.2 + - - +
84B ALA* 3.3 6.9 + - - +
85B GLN* 3.0 34.0 + - + +
232B ARG* 4.5 16.8 - - - +
258B ASP* 4.5 7.6 + - - +
286B VAL* 4.0 23.3 - - + -
288B ASP* 4.5 7.6 - - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLN* 3.1 2.3 + - + +
81B ALA* 1.3 77.9 - - - +
83B PHE* 1.3 95.0 + + + +
85B GLN* 3.4 8.2 + - + +
86B LEU* 2.9 49.7 + - + +
152B LEU* 4.7 6.5 - - + -
166B MSE 4.3 20.6 - - - -
258B ASP* 5.3 2.4 + - - +
284B ASP* 3.6 49.8 - - + +
286B VAL* 3.9 9.3 - - + +
301B PRO* 4.1 22.0 - - + -
303B ARG* 5.2 11.2 - - + -
306B ILE* 5.0 4.7 - - + -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.0 21.1 - - + +
76B PRO* 3.8 37.7 - - + -
77B GLU 3.7 16.8 - - - +
78B LEU* 4.4 2.1 - - - +
80B GLN* 3.0 34.1 + - + +
82B PHE* 1.3 102.8 - + + +
84B ALA* 1.3 63.2 + - - +
86B LEU* 3.8 9.7 - - + +
87B ALA* 2.8 31.4 + - - +
131B ALA* 4.0 16.2 - - + -
133B LEU* 4.2 21.3 - - + -
152B LEU* 4.9 2.7 - - + -
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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
----------------------------------------------------------
78A LEU* 3.5 27.2 - - + +
79A GLY* 5.1 1.3 - - - -
84A ALA* 3.8 7.4 - - + -
78B LEU* 3.4 33.5 + - - +
80B GLN 3.0 7.7 + - - +
81B ALA* 3.3 9.8 + - - +
83B PHE* 1.3 78.1 - - - +
85B GLN* 1.3 58.2 + - + +
87B ALA* 3.4 1.7 + - - +
88B ASP* 2.9 28.9 + - - +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 4.9 15.6 - - - +
81B ALA* 3.0 24.9 + - + +
82B PHE* 3.8 7.1 - - - +
84B ALA* 1.3 77.0 - - + +
86B LEU* 1.3 62.1 + - - +
88B ASP* 3.4 8.0 + - - +
89B GLU* 3.1 22.9 + - - +
284B ASP 4.6 3.4 + - - -
285B ASP 3.3 22.8 + - - -
286B VAL* 3.4 10.6 - - - +
287B ALA* 2.9 34.5 + - - +
288B ASP* 5.3 0.3 - - - +
303B ARG* 4.3 29.7 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 6.1 3.6 - - + -
75B VAL* 5.7 3.4 - - + -
82B PHE* 2.9 37.2 + - + +
83B PHE* 3.9 14.4 - - + +
85B GLN* 1.3 75.0 - - - +
87B ALA* 1.3 65.0 + - - +
89B GLU* 3.1 4.6 + - + -
90B VAL* 2.9 35.0 + - + +
131B ALA* 5.3 2.9 - - + -
152B LEU* 3.5 31.4 - - + -
303B ARG* 4.1 25.7 - - + +
306B ILE* 3.9 23.1 - - + -
307B ALA* 4.4 9.0 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.9 9.0 - - + -
73B LEU* 3.7 29.4 - - + -
75B VAL* 5.3 2.4 - - + +
78B LEU* 3.9 20.4 - - + -
83B PHE 2.8 23.4 + - - +
84B ALA 3.7 4.0 - - - +
86B LEU* 1.3 71.4 - - - +
88B ASP* 1.3 58.2 + - - +
90B VAL* 3.3 1.3 + - - +
91B ILE* 2.9 38.9 + - + +
103B VAL* 5.6 0.4 - - + -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 3.5 16.8 - - - +
78A LEU* 4.1 3.0 - - + +
79A GLY* 3.0 28.6 + - - +
105A GLN* 3.1 35.9 + - - +
84B ALA 2.9 17.9 + - - +
85B GLN* 3.5 8.1 - - - +
87B ALA* 1.3 75.3 - - - +
89B GLU* 1.3 65.2 + - - +
92B ARG* 3.0 24.4 + - - +
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Residues in contact with GLU 89 (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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85B GLN 3.1 11.1 + - - +
86B LEU* 3.1 11.2 + - - +
88B ASP* 1.3 81.7 + - - +
90B VAL* 1.3 56.1 + - - +
92B ARG* 2.8 49.0 + - - +
93B VAL* 3.0 40.0 + - - +
303B ARG* 4.6 19.5 - - + +
304B HIS* 3.4 39.1 + - + +
307B ALA* 3.8 15.4 - - + +
308B ARG* 5.3 0.2 + - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.7 7.6 - - + -
73B LEU* 4.4 24.2 - - + -
86B LEU* 2.9 31.1 + - + +
87B ALA* 3.3 6.7 + - - +
89B GLU* 1.3 73.9 - - - +
91B ILE* 1.3 59.9 + - - +
93B VAL* 3.3 2.1 + - - +
94B ALA* 2.9 27.7 + - - +
101B VAL* 4.8 7.0 - - + -
129B LEU* 3.9 29.6 - - + -
307B ALA* 3.9 23.6 - - + -
310B ALA* 5.8 1.3 - - + -
311B VAL* 3.9 9.8 - - + +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.6 28.0 - - + -
103A VAL* 3.8 35.0 - - + +
104A GLU* 4.7 3.4 - - - +
105A GLN* 3.8 28.7 - - + +
121A ARG* 5.2 1.9 + - - +
73B LEU* 5.4 0.4 - - + -
87B ALA* 2.9 23.9 + - + +
88B ASP 3.8 3.6 - - - +
90B VAL* 1.3 75.7 - - + +
92B ARG* 1.3 58.4 + - - +
94B ALA* 3.4 1.7 + - - +
95B ALA* 2.9 30.1 + - + +
99B LEU 5.1 0.3 - - - +
101B VAL* 4.0 30.2 - - + +
103B VAL* 4.4 9.0 - - + -
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Residues in contact with ARG 92 (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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105A GLN* 4.1 7.2 - - - +
88B ASP* 3.0 21.1 + - - +
89B GLU* 2.8 42.5 + - - +
91B ILE* 1.3 74.9 - - - +
93B VAL* 1.3 68.0 + - - +
95B ALA* 3.2 7.5 + - - +
96B GLU* 2.9 54.1 + - + +
304B HIS* 5.0 4.4 - - - -
308B ARG* 3.8 19.4 - - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 3.0 34.2 + - - +
90B VAL 3.9 2.9 - - - +
92B ARG* 1.3 74.4 - - - +
94B ALA* 1.3 67.1 + - - +
96B GLU* 3.1 17.9 + - - +
97B GLN* 3.2 34.3 + - - +
307B ALA* 4.5 1.1 - - + +
308B ARG* 3.8 53.6 - - + +
311B VAL* 3.7 20.9 - - + -
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Residues in contact with ALA 94 (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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71B ILE* 4.3 10.8 - - + -
90B VAL 2.9 18.5 + - - +
91B ILE 3.7 2.2 - - - +
92B ARG 3.3 0.2 - - - -
93B VAL* 1.3 76.8 - - - +
95B ALA* 1.3 60.5 + - - +
97B GLN 3.0 9.4 + - - -
98B ASP 3.2 0.2 + - - -
99B LEU* 2.9 40.4 + - + +
101B VAL* 3.6 27.6 - - + -
311B VAL* 4.1 11.4 - - + +
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Residues in contact with ALA 95 (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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121A ARG* 3.7 30.2 + - - +
91B ILE* 2.9 20.4 + - + +
92B ARG* 3.6 7.4 - - + +
93B VAL 3.2 0.4 - - - -
94B ALA* 1.3 75.3 - - - +
96B GLU* 1.3 63.8 + - + +
98B ASP* 3.2 17.3 + - - +
99B LEU 3.7 0.6 + - - -
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Residues in contact with GLU 96 (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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92B ARG* 2.9 44.6 + - + +
93B VAL* 3.1 11.3 + - - +
95B ALA* 1.3 76.9 - - + +
97B GLN* 1.3 62.8 + - + +
98B ASP* 3.4 5.9 + - - +
308B ARG* 3.1 32.4 + - - +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.2 24.6 + - - +
94B ALA* 3.0 7.8 + - - +
96B GLU* 1.3 81.3 - - + +
98B ASP* 1.3 68.7 + - - +
99B LEU* 3.3 18.6 + - + +
308B ARG* 4.3 8.9 - - - +
311B VAL* 3.6 13.6 - - - +
312B THR* 3.2 27.7 + - - +
315B SER* 3.1 27.3 + - - +
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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
------------------------------------------------------------
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