Contacts of the strand formed by residues 187 - 195 (chain K) in PDB entry 6C0W
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 GLN 187 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88K MET* 3.3 27.2 - - - +
89K SER* 2.8 24.8 + - - +
90K LYS* 2.8 38.0 + - + +
180K THR* 3.9 3.8 - - - +
186K HIS* 1.3 79.9 - - + +
188K ILE* 1.3 69.5 + - - +
189K VAL* 4.2 17.8 - - + +
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Residues in contact with ILE 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 4.1 26.0 - - + -
87K GLN 3.5 9.6 - - - +
88K MET* 4.5 9.2 - - + -
176K GLY* 3.7 37.5 - - - +
177K GLN* 5.0 6.3 - - + +
179K LEU* 5.1 8.5 - - + -
180K THR* 3.5 16.2 - - + +
186K HIS 6.0 0.2 - - - +
187K GLN* 1.3 80.2 + - - +
189K VAL* 1.3 76.1 + - - +
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Residues in contact with VAL 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 3.3 23.3 - - - +
87K GLN* 3.0 43.9 + - + +
88K MET 6.4 0.2 - - - -
89K SER* 5.6 2.5 - - - +
187K GLN* 4.2 22.2 - - + +
188K ILE* 1.3 84.0 - - - +
190K LYS* 1.3 64.4 + - - +
191K MET* 4.5 20.6 - - + -
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Residues in contact with LYS 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K ASP* 4.4 9.2 - - - +
86K PHE* 3.6 34.1 - - + -
172K THR* 3.9 19.7 - - - +
189K VAL* 1.3 77.5 - - - +
191K MET* 1.3 70.5 + - - +
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Residues in contact with MET 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K ASP* 4.5 6.8 - - - +
85K VAL* 3.8 23.8 + - + +
86K PHE 6.1 0.9 - - - -
87K GLN* 3.3 28.3 - - + +
160K TYR* 4.4 10.5 - - + +
189K VAL* 4.2 17.5 - - + -
190K LYS* 1.3 84.6 - - - +
192K ASP* 1.3 64.2 + - - +
193K LEU* 3.2 31.0 + - + +
205K VAL* 6.2 0.4 - - - -
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Residues in contact with ASP 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K MET* 1.3 75.5 - - - +
193K LEU* 1.3 62.7 + - + +
194K ARG* 3.0 14.4 + - - +
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Residues in contact with LEU 193 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83K TRP 4.1 0.2 - - - +
84K ASP* 3.4 18.9 - - - +
85K VAL* 3.4 39.8 + - + +
191K MET* 3.2 30.1 - - + -
192K ASP* 1.3 76.1 - - + +
194K ARG* 1.3 58.5 + - - +
195K SER 4.2 1.1 - - - -
201K LEU* 3.9 11.8 - - + +
204K ILE* 3.7 38.4 - - + +
205K VAL* 4.9 4.9 - - + -
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Residues in contact with ARG 194 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J C 2.4 50.7 + - - -
25J T 4.3 13.0 + - - -
82K VAL* 3.8 17.9 - - + +
83K TRP 3.3 17.7 - - - +
84K ASP* 4.8 10.8 - - + +
165K SER* 4.9 8.3 - - - +
192K ASP 3.0 11.1 + - - +
193K LEU* 1.3 72.4 - - - +
195K SER* 1.3 60.4 + - - +
201K LEU* 4.9 0.2 - - - +
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Residues in contact with SER 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K VAL* 3.3 7.5 - - - +
83K TRP* 2.7 35.7 + - - +
193K LEU 4.2 1.0 - - - -
194K ARG* 1.3 75.0 - - - +
196K ARG* 1.3 66.9 + - - +
197K TYR* 3.7 12.0 + - - +
200K SER* 5.3 6.9 - - - -
201K LEU* 4.3 23.2 - - - +
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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