Contacts of the helix formed by residues 77 - 89 (chain B) in PDB entry 3KUD
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 SER 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY 3.5 2.8 + - - -
76B MET* 1.3 80.1 - - - +
78B LEU* 1.3 69.3 + - - +
79B HIS* 3.8 1.4 - - - +
80B ASP* 2.9 28.3 + - - -
81B CYS* 3.5 15.8 + - - +
114B TRP 3.6 5.6 - - - -
115B ASN* 3.0 38.9 + - - -
116B THR 3.4 15.3 - - - -
117B ASP* 4.6 1.1 - - - +
118B ALA* 3.9 1.0 - - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.1 0.2 - - + -
77B SER* 1.3 72.8 - - - +
79B HIS* 1.3 60.8 + - - +
80B ASP 3.4 0.2 - - - -
81B CYS* 3.6 21.4 - - - -
82B LEU* 3.0 39.9 + - + +
98B VAL* 4.1 9.2 - - + -
112B LEU* 3.4 23.1 - - + -
113B ASP 4.9 2.5 - - - +
114B TRP* 3.5 20.6 + - + +
116B THR 3.1 8.9 + - - +
117B ASP 3.3 16.6 - - - +
118B ALA* 3.7 6.3 - - - -
121B LEU* 3.2 23.1 - - + -
126B LEU* 3.3 32.8 - - + -
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 3.8 7.2 - - - +
78B LEU* 1.3 76.2 - - - +
80B ASP* 1.3 67.7 + - - +
83B MET* 2.8 60.7 + - + +
93B PRO* 3.8 31.3 - - + +
94B GLU* 5.9 5.8 - - + -
114B TRP* 3.2 40.0 + - + +
115B ASN* 4.1 7.4 - - - +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY 4.8 1.0 - - - +
76B MET* 3.8 35.1 - - + +
77B SER* 2.9 27.0 + - - +
78B LEU 3.4 0.2 - - - -
79B HIS* 1.3 90.8 - - - +
81B CYS* 1.3 62.3 + - - +
82B LEU 3.3 0.7 + - - -
83B MET* 4.1 6.2 + - - +
84B LYS* 4.7 6.2 + - - +
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.6 25.1 - - + -
70B VAL* 3.4 29.8 - - + +
71B ASN 5.2 3.8 - - - +
72B VAL* 5.0 4.5 - - + -
76B MET* 4.1 21.2 - - + +
77B SER 3.5 9.9 + - - +
78B LEU* 3.6 19.3 - - - -
79B HIS 3.5 0.2 - - - -
80B ASP* 1.3 76.8 - - - +
82B LEU* 1.3 81.1 + - - +
84B LYS* 5.3 2.0 - - - +
85B LYS* 4.3 3.5 + - - +
118B ALA* 4.6 5.4 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.6 2.2 - - + -
60B VAL* 3.5 50.7 - - + -
62B LEU* 4.1 1.8 - - + -
68B THR* 4.0 6.3 - - + -
70B VAL* 3.8 6.3 - - + -
78B LEU* 3.0 25.2 + - + +
81B CYS* 1.3 102.7 - - - +
83B MET* 1.4 56.5 + - - +
84B LYS 3.3 2.9 - - - -
85B LYS* 2.7 44.3 + - + +
86B LEU* 3.0 27.8 + - + +
98B VAL* 6.0 1.1 - - + -
114B TRP* 4.0 14.8 - - + -
126B LEU* 4.9 0.4 - - + -
128B VAL* 4.8 2.9 - - + -
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 2.8 46.3 + - + +
80B ASP* 4.1 3.8 + - - +
81B CYS 3.9 0.2 - - - -
82B LEU* 1.4 67.3 - - - +
84B LYS* 1.3 62.1 + - - +
86B LEU* 4.3 5.3 - - - +
87B LYS* 3.1 61.9 + - + +
93B PRO* 3.8 29.1 - - + +
114B TRP* 5.6 0.8 - - - -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 5.6 3.2 - - - -
29A VAL* 5.8 0.2 - - - +
31A GLU* 2.8 43.6 + - + +
33A ASP* 5.8 4.7 - - + +
80B ASP 4.7 7.1 + - - +
81B CYS 5.7 2.5 - - - +
82B LEU 3.3 0.8 - - - -
83B MET* 1.3 81.1 - - - +
85B LYS* 1.3 67.0 + - + +
87B LYS* 4.6 2.1 - - - +
88B VAL* 3.1 32.9 + - + +
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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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33A ASP* 4.1 19.5 + - - +
35A THR* 6.3 1.0 - - - +
38A ASP* 3.7 24.7 + - - +
40A TYR* 5.1 3.6 + - - +
62B LEU* 4.2 6.1 - - + -
68B THR* 3.2 35.8 + - + +
69B VAL 4.7 2.7 + - - -
70B VAL* 3.9 23.3 - - + -
81B CYS 4.3 4.0 + - - +
82B LEU* 2.7 32.7 + - + +
84B LYS* 1.3 74.5 - - + +
86B LEU* 1.3 60.3 + - - +
88B VAL* 2.9 23.7 - - + +
89B ARG* 3.4 17.0 - - - +
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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
----------------------------------------------------------
62B LEU* 3.8 26.9 - - + -
82B LEU* 3.0 43.2 + - + +
83B MET* 3.8 4.7 + - - +
85B LYS* 1.3 76.8 - - - +
87B LYS* 1.3 53.8 + - - +
89B ARG* 2.8 39.0 + - - +
91B LEU* 3.3 30.4 + - + +
93B PRO* 4.3 20.4 - - + -
96B CYS* 3.8 29.8 - - + -
114B TRP* 4.3 10.8 - - + -
128B VAL* 4.1 11.9 - - + -
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.6 10.2 + - - +
83B MET* 3.1 50.8 + - + +
84B LYS* 4.6 2.5 - - - +
85B LYS 3.5 0.2 - - - -
86B LEU* 1.3 77.0 - - - +
88B VAL* 1.3 59.5 + - - +
90B GLY* 3.4 10.6 + - - -
91B LEU 3.5 18.2 - - - +
92B GLN* 6.0 0.2 - - - -
93B PRO* 4.2 10.8 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.1 34.3 - - + -
24A ILE* 3.4 19.5 - - - +
25A GLN* 3.1 25.6 + - + +
27A HIS* 4.8 12.3 - - + +
29A VAL* 5.0 4.3 - - + -
40A TYR* 4.8 5.8 - - + +
84B LYS* 3.1 20.4 + - + +
85B LYS* 2.9 32.5 - - + +
87B LYS* 1.3 71.8 - - - +
89B ARG* 1.3 68.1 + - - +
90B GLY 3.1 2.0 + - - -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 5.0 5.2 - - - -
38A ASP* 3.1 20.6 + - - -
39A SER 3.2 16.4 + - - +
40A TYR* 3.0 39.7 + - + -
62B LEU* 3.3 24.0 - - + +
66B GLN* 3.7 31.1 - - - +
67B ARG 2.8 33.1 + - - -
68B THR* 4.0 0.2 - - - -
85B LYS* 3.4 24.9 + - - +
86B LEU* 2.8 17.0 + - - +
88B VAL* 1.3 77.2 - - - +
90B GLY* 1.3 50.5 + - - -
91B LEU* 2.8 33.3 + - + +
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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
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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