Contacts of the strand formed by residues 83 - 89 (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 TRP 83 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74K MET* 5.1 11.7 - - + -
78K GLN* 3.8 34.6 + - + +
81K LYS* 4.3 15.4 + - + -
82K VAL* 1.3 76.8 - - - +
84K ASP* 1.3 62.4 + - - +
132K TRP* 4.4 17.5 - + - -
151K TYR* 4.2 19.3 - + + -
153K VAL* 4.6 11.7 - - + -
162K PHE* 4.5 9.0 - - + -
163K THR 3.3 24.2 - - - +
164K SER* 3.6 28.3 - - - -
165K SER* 5.3 0.7 - - - -
194K ARG* 3.3 30.4 - - - +
195K SER 2.7 15.7 + - - +
196K ARG 3.3 28.6 + - - -
197K TYR 4.8 0.4 - - - -
198K LEU* 4.7 25.9 - - + +
201K LEU* 3.9 17.0 - - + -
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Residues in contact with ASP 84 (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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83K TRP* 1.3 75.9 - - - +
85K VAL* 1.3 83.6 + - - +
86K PHE* 3.5 26.3 - - - -
162K PHE* 3.3 5.4 - - - +
163K THR* 2.5 56.0 + - + +
165K SER* 5.0 8.7 - - - +
190K LYS* 4.4 9.1 - - - +
191K MET 4.5 8.3 - - - +
193K LEU 3.4 11.9 - - - +
194K ARG* 4.8 9.7 - - + +
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Residues in contact with VAL 85 (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* 1.3 87.4 + - - +
86K PHE* 1.3 82.2 + - - +
160K TYR* 4.5 4.9 - - + -
161K ALA 3.7 2.7 - - - -
162K PHE* 3.9 23.3 - - + -
191K MET* 3.8 25.4 + - + +
193K LEU* 3.4 35.3 + - + +
201K LEU* 3.7 29.8 - - + -
205K VAL* 4.3 16.6 - - + -
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Residues in contact with PHE 86 (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* 3.5 24.7 - - - -
85K VAL* 1.3 86.7 - - - +
87K GLN* 1.3 65.3 + - - +
88K MET* 6.4 0.2 - - + -
160K TYR* 3.5 10.7 - - - -
161K ALA* 2.9 39.6 + - + +
163K THR* 3.4 31.0 - - + -
172K THR* 4.5 18.4 - - + -
175K LEU* 5.6 9.9 - - + -
176K GLY* 5.6 2.7 - - - -
188K ILE* 4.1 24.2 - - + -
189K VAL* 3.3 20.2 - - - +
190K LYS* 3.6 33.9 - - + -
191K MET* 6.1 1.1 - - - -
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Residues in contact with GLN 87 (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* 1.3 79.5 - - - +
88K MET* 1.3 76.5 + - - +
89K SER* 5.8 2.5 - - - -
159K PRO* 3.5 22.9 - - + +
160K TYR* 3.2 47.0 + - + -
161K ALA* 6.1 0.2 - - - -
187K GLN 4.7 0.2 - - - -
188K ILE* 3.5 3.3 - - - +
189K VAL* 3.0 44.1 + - + +
191K MET* 3.3 18.7 - - + +
209K TYR* 5.8 1.4 - - - -
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Residues in contact with MET 88 (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* 6.4 0.2 - - + -
87K GLN* 1.3 86.4 + - - +
89K SER* 1.3 65.1 + - - +
154K TYR* 3.7 31.6 - - + +
159K PRO* 3.0 35.9 + - - +
161K ALA* 5.9 1.8 - - + -
179K LEU* 3.7 26.0 - - + +
180K THR* 3.8 14.8 - - - +
183K SER* 2.8 36.1 - - - +
185K HIS* 3.6 21.8 - - + +
187K GLN 3.3 15.0 - - - +
188K ILE* 4.5 9.2 - - + -
189K VAL* 6.4 0.7 - - - -
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Residues in contact with SER 89 (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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87K GLN* 5.8 2.9 - - - -
88K MET* 1.3 76.4 - - - +
90K LYS* 1.3 74.7 + - - +
91K GLY 3.6 2.5 - - - -
185K HIS* 3.1 16.0 - - - -
186K HIS 3.3 12.5 + - - -
187K GLN* 2.8 38.7 + - - +
189K VAL* 5.6 2.7 - - - +
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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