Contacts of the strand formed by residues 82 - 87 (chain H) in PDB entry 3KTM
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 ILE 82 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H PRO* 5.6 0.2 - - + -
70H LEU* 3.6 21.9 - - + +
73H CYS* 3.2 48.5 - - + +
74H GLN* 3.3 35.1 + - + +
77H TYR* 3.6 23.6 - - + +
80H LEU* 3.2 17.8 + - + +
81H GLN* 1.3 71.8 - - - +
83H THR* 1.3 61.9 + - - +
84H ASN 3.7 8.1 - - - +
117H CYS* 4.0 12.1 - - + -
118H LEU 3.3 15.5 - - - +
119H VAL* 4.3 5.8 - - + +
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Residues in contact with THR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G LEU 4.9 1.0 - - - +
30G ALA* 4.9 11.2 - - - +
31G GLU* 4.1 27.6 - - + +
70H LEU* 4.3 9.7 - - - +
81H GLN* 3.3 30.2 + - + +
82H ILE* 1.3 76.0 - - - +
84H ASN* 1.3 71.4 + - - +
118H LEU* 2.9 11.1 + - - +
119H VAL 4.1 0.7 - - - -
120H GLY 2.7 29.5 + - - +
122H PHE* 6.2 0.3 - - - +
176H ILE* 5.9 0.7 - - - +
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Residues in contact with ASN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LEU* 3.8 12.0 - - - +
82H ILE* 3.7 4.5 - - - +
83H THR* 1.3 82.1 + - - +
85H VAL* 1.3 87.0 + - - +
118H LEU* 2.8 43.3 + - + +
122H PHE* 6.1 1.1 - - + -
173H PRO* 4.1 19.0 - - - +
175H GLY 3.0 24.2 + - - -
176H ILE* 3.4 8.6 - - - +
177H ASP* 2.8 23.5 + - - +
179H PHE* 4.9 4.7 - - - -
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H LYS* 4.1 20.6 - - + +
69H ILE* 4.2 13.9 - - + -
70H LEU* 3.6 26.7 - - + +
73H CYS* 3.8 22.9 - - - -
84H ASN* 1.3 102.7 + - - +
86H VAL* 1.3 63.3 + - - +
115H TYR* 4.6 6.5 - - + -
116H ARG 3.4 8.7 - - - +
118H LEU* 4.5 2.5 - - - +
176H ILE* 4.3 6.3 - - + -
177H ASP* 3.3 31.7 - - + +
179H PHE* 4.1 1.2 - - - -
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Residues in contact with VAL 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H VAL* 1.3 78.4 - - - +
87H GLU* 1.3 69.1 + - - +
115H TYR* 3.6 4.9 - - - -
116H ARG* 2.7 66.6 + - + +
118H LEU* 3.9 21.3 - - + -
122H PHE* 6.1 0.4 - - + -
147H HIS* 4.1 9.6 - - + +
170H MET* 3.9 28.3 - - + -
177H ASP* 3.9 9.4 - - - +
179H PHE* 3.9 13.2 - - + -
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Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H SO4 4.4 3.1 + - - -
66H LYS* 2.7 31.5 + - - -
86H VAL* 1.3 87.7 - - - +
88H ALA* 1.3 70.1 + - - +
89H ASN* 3.8 1.4 + - - +
113H ILE* 4.5 8.1 - - + -
114H PRO 3.7 7.6 - - - +
115H TYR* 3.3 23.1 + - + +
147H HIS* 3.1 46.4 + - + +
177H ASP* 2.9 21.6 - - - +
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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