Contacts of the strand formed by residues 82 - 87 (chain A) in PDB entry 3KDH
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 VAL 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.4 6.4 - - - -
73A ILE* 2.8 44.0 + - + -
74A SER* 2.9 20.5 + - - +
80A GLY 3.7 9.4 - - - +
81A SER* 1.3 78.1 - - - +
83A ARG* 1.3 61.5 + - - +
97A THR* 3.4 31.9 - - + -
98A GLU 3.3 8.7 - - - +
99A ARG* 3.8 22.0 - - + +
115A VAL* 5.8 2.5 - - + -
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Residues in contact with ARG 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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54A ILE 5.5 2.0 + - - -
56A ARG 5.0 0.4 + - - -
57A PHE* 2.9 58.7 + - + +
60A PRO* 4.1 18.0 - - - +
63A TYR* 6.3 0.4 - - - -
64A LYS* 3.6 20.8 - - - +
70A CYS* 3.8 12.3 - - - -
71A ARG 3.3 10.3 - - - +
72A LEU* 3.8 13.5 - - + -
82A VAL* 1.3 75.3 - - - +
84A GLU* 1.3 61.1 + - - +
85A VAL* 3.7 16.5 - - + +
96A SER 3.5 0.5 - - - +
97A THR* 3.4 5.0 - - - +
98A GLU* 2.8 65.1 + - + +
110A LEU* 6.0 0.6 - - - +
112A PHE* 3.8 22.8 - - - -
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Residues in contact with GLU 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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69A ARG* 3.9 1.0 - - - +
70A CYS* 3.3 4.5 - - - -
71A ARG* 2.8 58.8 + - + +
73A ILE* 3.6 40.0 - - + +
82A VAL 4.4 0.4 + - - -
83A ARG* 1.3 71.4 - - - +
85A VAL* 1.3 62.1 + - - +
86A THR* 4.1 2.6 + - - +
95A THR* 4.0 18.9 + - + +
96A SER 3.5 2.7 - - - -
97A THR* 4.0 15.7 + - - +
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Residues in contact with VAL 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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60A PRO* 4.4 7.0 - - + -
67A VAL* 3.9 29.4 - - + -
69A ARG 3.5 3.1 - - - +
70A CYS* 3.9 7.6 - - + -
83A ARG* 3.7 22.0 - - + +
84A GLU* 1.3 75.2 - - - +
86A THR* 1.3 64.6 + - - +
87A VAL* 3.7 19.2 + - + -
94A SER 3.7 0.3 - - - +
95A THR* 3.3 3.0 - - - -
96A SER* 2.7 52.0 + - - +
98A GLU* 3.7 24.9 - - - +
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Residues in contact with THR 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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67A VAL* 3.7 4.0 - - - +
68A LYS* 2.7 56.4 + - + -
69A ARG* 2.7 38.5 + - + +
84A GLU* 4.1 2.5 + - - +
85A VAL* 1.3 73.7 - - - +
87A VAL* 1.3 58.1 + - - +
93A ALA* 4.1 13.5 - - + -
94A SER 3.4 11.4 - - - +
95A THR* 4.0 12.1 + - - +
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Residues in contact with VAL 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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66A PHE* 3.3 18.8 - - + +
67A VAL* 5.1 3.6 - - + -
85A VAL* 3.7 26.5 - - + +
86A THR* 1.3 78.5 - - - +
88A ILE* 1.3 78.0 + - - +
89A SER* 5.3 2.8 + - - -
92A PRO 4.7 0.3 - - - +
93A ALA* 3.3 5.4 - - - -
94A SER* 2.8 41.4 + - - +
96A SER* 4.6 9.6 - - - -
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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