Contacts of the strand formed by residues 75 - 79 (chain A) in PDB entry 1KPI
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 THR 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLY 4.4 1.0 + - - -
74A MET* 1.3 75.6 - - - +
76A LEU* 1.3 66.7 + - - +
97A ASN* 3.4 11.4 + - + +
99A ILE* 4.1 24.0 - - + -
123A ARG* 3.2 29.1 + - - +
137A PRO 4.9 4.0 - - - +
138A VAL* 4.0 15.4 - - + +
139A ASP* 2.7 38.9 + - - +
140A ARG* 3.5 7.8 + - - +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.9 15.3 - - + -
68A LEU* 3.6 28.5 - - + -
70A LEU* 4.2 8.7 - - + -
74A MET 3.9 0.8 + - - -
75A THR* 1.3 77.9 - - - +
77A LEU* 1.3 65.6 + - - +
78A ASP* 4.8 2.0 - - + +
86A THR* 5.2 1.3 - - + +
87A MET* 5.8 0.9 - - - -
90A ALA* 3.3 33.7 - - + -
96A VAL* 4.0 11.2 - - + -
97A ASN 2.6 15.3 + - - +
98A VAL* 3.2 10.5 - - + +
99A ILE* 2.9 26.3 + - - +
140A ARG* 3.5 22.4 - - + +
141A ILE 4.2 0.2 - - - +
142A VAL* 4.1 15.9 - - + -
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Residues in contact with LEU 77 (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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75A THR 4.1 0.2 + - - -
76A LEU* 1.3 73.3 - - - +
78A ASP* 1.3 59.6 + - - +
79A ILE* 3.6 26.6 + - + -
99A ILE* 3.5 19.7 - - + +
101A LEU* 3.7 28.0 - - + -
134A PHE* 4.0 25.6 - - + -
138A VAL* 4.2 16.6 - - + -
140A ARG 3.0 14.3 + - - +
141A ILE* 3.4 12.0 - - + +
142A VAL* 2.8 31.2 + - - +
169A PHE* 3.9 22.9 - - + -
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Residues in contact with ASP 78 (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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76A LEU* 4.1 3.7 + - + -
77A LEU* 1.3 73.4 - - - +
79A ILE* 1.3 60.7 + - - +
80A GLY 3.3 6.2 + - - +
81A CYS* 3.4 33.3 + - + +
86A THR* 3.3 27.1 + - + -
87A MET* 3.7 19.7 + - + +
98A VAL* 6.0 0.9 - - + -
99A ILE 2.9 14.5 + - - +
101A LEU* 3.0 26.5 + - - +
142A VAL* 3.3 22.4 - - + +
143A SER* 4.9 1.4 - - - -
144A LEU* 5.1 1.8 + - - +
900A SAH 4.6 3.7 + - - -
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Residues in contact with ILE 79 (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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77A LEU* 3.6 20.9 - - + -
78A ASP* 1.3 69.1 - - - +
80A GLY* 1.3 65.5 + - - +
101A LEU* 4.3 10.8 - - + -
131A TRP* 3.9 15.9 - - + -
141A ILE* 3.6 25.1 - - + -
142A VAL 2.9 8.9 + - - -
143A SER* 3.0 31.2 + - - +
146A ALA* 3.5 4.2 - - - +
150A PHE* 3.4 29.2 - - + -
165A PHE* 4.0 13.2 - - + -
169A PHE* 3.8 31.2 - - + -
900A SAH 4.6 4.7 - - + -
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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