Contacts of the strand formed by residues 91 - 96 (chain C) in PDB entry 3KXC
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 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C THR* 3.3 6.4 + - - -
87C ASN* 3.1 48.4 + - - +
89C GLN 5.1 2.0 - - - +
90C GLY* 1.3 84.4 - - - +
92C TYR* 1.3 68.2 + - - +
93C VAL* 4.7 4.7 - - + +
152C GLN* 3.7 36.3 - - + +
153C VAL 3.3 4.5 - - - +
154C MET* 4.4 25.4 - - + -
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 2.6 34.4 + - - +
62C LEU* 3.3 30.4 + - + +
65C MET* 3.7 32.5 - - + -
84C LEU* 3.9 15.3 - - + -
85C ARG 3.3 7.4 - - - +
86C THR* 3.5 30.5 + - - -
88C HIS* 5.6 1.6 - - - -
90C GLY* 4.7 5.4 - - - -
91C ILE* 1.3 77.5 - - - +
93C VAL* 1.3 65.5 + - - +
94C LEU* 4.0 17.3 - - + -
151C PHE 3.7 0.2 - - - +
152C GLN* 3.4 5.4 - - - +
153C VAL* 2.8 38.4 + - + +
155C ILE* 3.4 23.8 - - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ASN 3.6 1.9 - - - +
84C LEU* 3.6 4.0 - - - +
85C ARG* 2.9 56.2 + - + +
91C ILE* 4.7 4.7 - - + -
92C TYR* 1.3 78.4 - - - +
94C LEU* 1.3 65.5 + - - +
95C GLN 4.0 0.8 + - - +
150C LYS* 4.0 37.9 - - + -
151C PHE 3.4 5.4 - - - +
152C GLN* 4.3 23.8 - - + +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C MET* 3.8 25.8 - - + -
68C ILE* 3.9 28.0 - - + -
69C CYS* 3.9 21.5 - - - -
73C TRP* 4.8 1.1 - - + -
81C ILE* 3.7 20.6 - - + -
83C ASN 3.6 3.8 - - - -
84C LEU* 3.9 8.7 - - + +
92C TYR* 4.0 4.5 - - + -
93C VAL* 1.3 77.2 - - - +
95C GLN* 1.3 60.3 + - - +
126C ILE* 4.4 17.3 - - + -
149C CYS 3.8 0.9 - - - +
150C LYS* 3.4 4.8 - - - -
151C PHE* 2.8 47.8 + - + +
153C VAL* 4.0 17.3 - - + -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ILE* 3.3 4.3 - - - +
82C ASP* 2.8 32.9 + - - +
83C ASN* 2.8 36.5 + - + +
85C ARG* 3.0 31.9 + - - +
93C VAL* 4.0 0.6 + - + -
94C LEU* 1.3 74.2 - - - +
96C ASP* 1.3 57.8 + - - +
97C ASN* 2.8 25.6 + - - +
144C SER* 5.3 4.3 - - - +
148C ALA* 5.5 2.0 - - + +
149C CYS 3.5 9.6 - - - +
150C LYS* 3.3 29.7 - - + +
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Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TRP* 2.9 28.2 + - + +
77C PHE* 5.1 0.9 - - - -
79C LYS* 2.7 37.0 + - - -
80C GLN 5.6 0.9 - - - -
81C ILE* 4.1 12.8 - - + -
82C ASP* 3.6 4.0 - - - +
94C LEU 4.0 1.0 + - - -
95C GLN* 1.3 73.4 - - - +
97C ASN* 1.3 62.3 + - - +
98C LYS 2.9 8.0 + - - -
99C PHE* 3.5 28.7 + - + -
100C ARG 4.7 0.2 + - - -
148C ALA* 3.3 0.2 - - - -
149C CYS 2.9 36.9 + - - +
151C PHE* 4.8 3.4 - - + -
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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