Contacts of the helix formed by residues 79 - 88 (chain A) in PDB entry 2KBX
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 HIS 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU 4.6 0.4 + - - -
45A GLY* 3.2 43.9 + - - -
47A SER* 5.8 1.6 - - - -
74A ALA 4.5 2.4 + - - -
77A HIS* 2.9 30.0 + + + +
78A GLY* 1.3 80.3 + - - +
80A ARG* 1.3 70.6 + - - +
81A ASP* 3.0 3.7 + - + +
82A ILE* 3.2 25.5 + - + +
83A VAL* 3.2 21.5 + - - +
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Residues in contact with ARG 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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78A GLY 3.6 14.0 + - - -
79A HIS* 1.3 71.3 - - - +
81A ASP* 1.3 64.8 + - - +
83A VAL* 3.3 3.7 + - - +
84A GLN* 3.1 32.8 + - + +
112A GLN* 2.5 35.9 + - - +
113A ASP* 5.8 2.0 + - - -
114A GLN* 5.2 14.8 - - + +
115A VAL* 3.7 25.9 - - + +
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Residues in contact with ASP 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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47A SER* 4.3 18.2 + - - -
79A HIS* 3.0 2.8 + - + -
80A ARG* 1.3 78.1 - - - +
82A ILE* 1.3 67.6 + - - +
84A GLN* 3.0 26.0 + - - +
85A LYS* 3.2 20.9 + - - +
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Residues in contact with ILE 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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41A ALA 5.1 1.3 - - - +
42A CYS* 3.9 32.1 - - - +
45A GLY* 5.3 5.8 - - - -
47A SER* 4.6 18.5 - - - +
50A VAL* 4.2 26.2 - - + -
74A ALA* 4.7 13.2 - - + +
77A HIS* 5.7 1.1 - - + -
79A HIS* 3.2 32.2 + - + +
81A ASP* 1.3 79.5 + - - +
83A VAL* 1.3 64.7 + - + +
85A LYS* 3.1 15.7 - - + +
86A LEU* 2.6 48.5 + - + +
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Residues in contact with VAL 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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74A ALA* 4.0 30.7 - - + +
75A ALA* 4.4 11.7 - - + +
78A GLY 5.6 0.4 - - - -
79A HIS 3.2 17.5 - - - +
80A ARG* 3.3 11.0 - - - +
81A ASP 3.0 0.4 + - - -
82A ILE* 1.3 84.8 - - + +
84A GLN* 1.3 58.9 + - + +
86A LEU* 4.1 6.1 - - + -
87A LEU* 2.5 54.4 + - + +
115A VAL* 4.4 24.7 - - + +
118A ASP* 6.3 3.4 - - + -
119A LEU* 5.7 4.5 - - + -
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Residues in contact with GLN 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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80A ARG* 3.3 26.0 - - - +
81A ASP* 3.0 15.5 + - - +
83A VAL* 1.3 78.7 - - + +
85A LYS* 1.3 59.7 + - - +
87A LEU* 3.8 4.7 - - - -
88A GLN* 2.9 53.1 + - - +
115A VAL* 6.4 1.3 - - + -
118A ASP* 4.8 14.1 - - + +
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Residues in contact with LYS 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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47A SER* 4.8 7.2 - - - -
50A VAL* 5.8 0.8 - - - +
51A GLU* 3.3 45.8 - - - +
54A ILE* 4.5 13.7 - - - +
81A ASP* 3.4 22.2 + - - +
82A ILE* 3.1 29.7 - - + +
84A GLN* 1.3 78.1 - - - +
86A LEU* 1.3 59.3 + - + +
88A GLN* 3.9 6.1 - - - -
89A TYR* 2.6 57.0 + - + -
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Residues in contact with LEU 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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38A LEU* 6.4 0.9 - - + -
42A CYS* 5.7 1.8 - - - -
54A ILE* 4.3 12.1 - - + -
60A ILE* 3.5 40.3 - - + +
70A PRO* 4.7 6.5 - - + -
71A LEU* 3.4 33.0 - - + +
74A ALA* 4.1 23.6 - - + -
82A ILE* 2.6 38.9 + - + +
83A VAL* 3.7 4.0 - - + +
85A LYS* 1.3 77.6 - - + +
87A LEU* 1.3 63.2 + - + +
88A GLN 3.7 0.2 + - - -
89A TYR* 3.9 11.7 + - + +
90A LYS 4.7 1.6 + - - -
92A ASP* 4.9 0.9 - - - +
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Residues in contact with LEU 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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71A LEU* 5.1 11.7 - - + -
83A VAL* 2.5 33.4 + - + +
84A GLN* 4.7 1.8 - - - +
86A LEU* 1.3 78.5 - - + +
88A GLN* 1.3 67.8 + - + +
89A TYR 3.3 3.6 - - - -
91A ALA* 3.4 31.5 + - + +
93A ILE* 4.6 12.1 - - + -
103A PRO* 5.6 0.7 - - + -
118A ASP* 3.3 28.3 - - + +
119A LEU* 3.3 43.1 - - + -
122A ASN* 6.3 1.6 - - - +
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Residues in contact with GLN 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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84A GLN* 2.9 44.7 + - - +
85A LYS* 3.9 5.9 + - - -
86A LEU 3.3 0.4 - - - -
87A LEU* 1.3 89.1 - - + +
89A TYR* 1.3 67.1 + - + +
91A ALA* 4.7 1.8 - - - -
118A ASP* 4.2 14.5 + - - +
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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