Contacts of the strand formed by residues 92 - 97 (chain C) in PDB entry 1KXT
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 ARG 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C GLN 3.1 19.8 + - - -
6C THR* 3.6 10.0 - - - +
7C GLN* 4.4 18.8 - - - +
38C GLY 3.1 15.3 + - - +
39C GLY* 3.1 0.7 - - - -
40C VAL 2.7 29.1 + - - -
87C ASN* 3.2 42.4 + - - +
90C GLY* 4.3 13.0 - - - -
91C VAL* 1.3 77.2 - - - +
93C ILE* 1.3 61.5 + - - +
94C TYR* 3.2 34.5 - - + +
192C ALA* 3.6 6.7 - - + -
221C TRP* 4.2 15.8 + - - +
222C PHE* 3.1 36.3 - - - -
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Residues in contact with ILE 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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24C ILE* 4.3 11.7 - - + -
28C CYS* 5.0 0.2 - - - -
40C VAL* 3.3 30.3 - - + -
42C VAL* 3.8 29.4 - - + -
79C PHE* 4.7 4.7 - - + -
82C MET* 4.0 22.7 - - + -
83C VAL* 4.5 22.4 - - + +
86C CYS* 4.3 21.1 - - + -
87C ASN* 5.1 3.1 + - - +
91C VAL 4.6 0.2 - - - +
92C ARG* 1.3 78.0 - - - +
94C TYR* 1.3 67.4 + - - +
95C VAL* 4.7 2.7 - - + +
190C GLY 5.7 0.6 + - - -
191C VAL* 3.1 10.2 - - + +
192C ALA* 3.0 26.8 + - - +
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Residues in contact with TYR 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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4C PRO 2.6 30.2 + - - -
6C THR* 3.2 19.2 - - + +
13C ILE* 3.5 32.3 - - + -
39C GLY* 3.8 2.5 - - - -
40C VAL 2.8 19.7 + - - +
41C GLN* 3.2 9.9 - - + +
42C VAL* 3.0 24.3 + - - -
92C ARG* 3.2 29.7 - - + +
93C ILE* 1.3 73.2 - - - +
95C VAL* 1.3 64.3 + - - +
192C ALA* 3.6 11.2 - - + -
193C GLY* 3.2 29.4 - - - +
194C PHE* 4.5 0.7 - - - +
229C PHE* 3.6 25.6 - + + -
231C PHE* 4.2 18.4 - + + -
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Residues in contact with VAL 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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42C VAL* 3.8 10.8 - - + -
45C PRO* 3.3 31.4 - - + -
79C PHE* 3.8 28.3 - - + -
93C ILE* 4.7 1.3 - - + -
94C TYR* 1.3 73.4 - - - +
96C ASP* 1.3 65.2 + - - +
97C ALA* 3.3 3.7 + - + +
182C TYR* 4.2 5.4 - - - +
186C LEU* 4.1 10.5 - - + -
191C VAL* 3.9 20.1 - - + +
193C GLY 3.0 6.3 + - - -
194C PHE* 3.1 24.8 - - + +
195C ARG* 2.9 29.2 + - - -
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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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15C HIS* 5.5 0.5 - - - -
41C GLN* 4.5 8.8 + - + +
42C VAL 3.2 22.4 + - - +
43C SER* 4.4 0.7 - - - -
44C PRO* 3.5 32.6 - - + +
45C PRO* 4.1 1.0 - - - +
46C ASN* 4.9 0.3 - - - +
62C TYR* 2.6 31.8 + - - -
94C TYR 3.8 0.2 + - - -
95C VAL* 1.3 74.8 - - - +
97C ALA* 1.3 61.7 + - - +
98C VAL* 3.5 2.9 + - - +
195C ARG* 2.9 45.7 + - - +
197C ASP* 3.6 10.7 - - - +
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Residues in contact with ALA 97 (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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95C VAL* 3.3 4.9 + - + -
96C ASP* 1.3 70.0 - - - +
98C VAL* 1.3 62.2 + - - +
99C ILE* 3.5 17.3 + - + +
182C TYR* 4.9 5.8 - - + -
183C LEU* 3.9 28.7 - - + -
194C PHE* 4.5 12.8 - - + -
195C ARG 3.0 13.3 + - - +
196C ILE* 4.1 9.2 - - + -
197C ASP* 3.0 25.3 + - - +
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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