Contacts of the strand formed by residues 207 - 212 (chain B) in PDB entry 2KH2
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B SER* 4.1 7.3 - - - -
151B CYS 2.7 30.7 + - - -
152B ALA* 3.7 5.3 + - - +
158B PHE* 3.8 5.1 - - - -
202B ASP* 2.9 31.7 + - + +
205B LYS* 3.9 19.5 - - + -
206B ASN* 1.3 78.8 - - - +
208B LEU* 1.3 63.4 + - - +
209B TYR* 3.6 36.9 + - + +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 5.9 0.9 - - + -
149B LEU 3.5 0.9 - - - +
150B SER* 3.1 10.0 - - - -
151B CYS* 2.9 33.9 + - + +
153B ALA* 5.8 1.1 - - + -
158B PHE* 3.7 26.9 - - + -
163B MET* 3.5 38.4 - - + -
164B SER 5.4 0.7 - - - +
165B TRP* 3.9 26.7 - - + +
180B ILE* 3.8 22.4 - - + -
200B SER 3.7 3.6 - - - +
201B ARG* 4.0 4.3 - - + -
207B THR* 1.3 74.1 - - - +
209B TYR* 1.3 61.0 + - - +
210B LEU 4.1 0.2 - - - -
225B CYS* 3.7 29.4 - - - -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG* 3.3 39.7 - - + -
149B LEU 3.5 1.6 - - - -
150B SER* 3.6 16.8 - - - -
165B TRP* 5.1 1.6 - - - -
180B ILE* 5.1 0.3 - - - +
198B THR 3.9 0.2 - - - +
199B ILE* 3.6 4.0 - - - +
200B SER* 2.7 59.1 + - - +
201B ARG 4.9 0.7 - - - -
202B ASP* 3.8 24.7 - - + -
205B LYS* 3.6 24.3 - - - +
207B THR* 3.6 23.8 - - + +
208B LEU* 1.3 75.0 - - - +
210B LEU* 1.3 61.2 + - - +
211B GLN* 3.9 1.4 + - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU 3.5 1.7 - - - +
148B ARG* 3.4 5.9 - - - +
149B LEU* 2.8 60.5 + - + +
165B TRP* 3.9 43.3 - - + +
177B VAL* 4.6 8.3 - - + -
178B ALA* 5.0 0.7 - - + -
197B PHE* 4.3 18.4 - - + -
198B THR 3.8 5.4 - - - +
199B ILE* 3.8 25.8 - - + -
208B LEU 4.1 0.6 + - - -
209B TYR* 1.3 71.7 - - - +
211B GLN* 1.3 59.8 + - - +
212B MET* 3.5 14.0 + - + +
223B TYR* 4.1 14.6 - - + -
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B SER* 4.3 22.0 - - - -
147B LEU 4.3 6.0 + - - +
148B ARG* 3.5 24.7 - - - +
196B ARG 4.0 0.2 - - - +
197B PHE* 3.4 6.8 - - - +
198B THR* 2.8 51.0 + - + +
200B SER* 6.0 1.8 - - - +
209B TYR 3.9 1.4 + - - -
210B LEU* 1.3 70.6 - - - +
212B MET* 1.3 63.0 + - - +
213B ASN* 3.9 14.6 + - + +
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Residues in contact with MET 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLY 4.1 0.2 - - - +
146B SER* 3.1 9.8 - - - -
147B LEU* 2.9 47.3 + - - +
149B LEU* 3.6 33.7 - - - -
196B ARG 4.0 3.8 - - - -
197B PHE* 3.7 17.7 - - + -
210B LEU* 3.9 11.9 - - + +
211B GLN* 1.3 74.1 + - - +
213B ASN* 1.3 61.7 + - - +
215B LEU* 3.6 36.7 - - + +
219B ASP 5.3 0.7 - - - +
223B TYR* 3.6 36.3 - - + +
244B VAL* 4.2 10.5 - - + -
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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