Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 3C6Q
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 LYS 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B MET* 5.0 3.6 - - - -
119B LEU* 4.3 31.6 + - + +
120B LEU* 3.9 22.2 - - + +
184B ASP 2.9 12.9 + - - +
185B ALA* 3.1 10.4 - - + -
186B PHE 2.8 25.3 + - - -
208B GLY* 2.6 28.5 + - - +
209B LYS 4.1 5.4 + - - +
210B VAL* 1.3 75.2 - - - +
212B ILE* 1.3 64.1 + - - +
231B GLN* 3.3 28.9 - - + +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 3.5 10.3 - - + +
194B GLY* 4.3 8.1 - - - +
197B GLN* 3.7 22.4 - - + +
198B ALA* 3.5 38.6 - - + +
201B VAL* 3.7 21.5 - - + -
210B VAL 4.1 5.6 - - - +
211B LYS* 1.3 82.0 - - - +
213B VAL* 1.3 73.6 + - - +
229B VAL* 4.0 19.1 - - + +
230B ILE* 3.8 18.8 - - + +
231B GLN* 2.9 28.7 + - - +
232B ALA 3.6 4.4 + - - +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.9 35.0 - - + +
115B ILE* 4.0 24.5 - - + -
116B MET* 4.0 32.8 - - + -
119B LEU* 4.5 12.1 - - + -
186B PHE 3.1 5.5 + - - -
187B PHE* 3.1 13.8 - - + -
188B GLY 2.9 20.8 + - - -
211B LYS* 5.5 0.2 - - + -
212B ILE* 1.3 79.3 - - - +
214B CYS* 1.3 67.9 + - - +
232B ALA* 3.1 14.8 - - + +
234B MET* 4.8 2.2 - - - -
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Residues in contact with CYS 214 (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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187B PHE* 4.6 1.1 - - - -
188B GLY 3.2 17.5 - - - +
194B GLY* 3.7 35.2 - - - +
212B ILE* 4.5 1.8 - - + -
213B VAL* 1.3 80.9 - - - +
215B PHE* 1.3 64.9 + - - +
221B ILE* 4.7 4.0 - - - -
230B ILE* 3.9 21.5 - - - -
232B ALA 3.1 7.7 + - - -
233B THR* 3.1 20.3 - - - -
234B MET* 2.8 35.7 + - - +
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Residues in contact with PHE 215 (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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103B THR* 5.8 0.7 - - + -
105B ASN* 5.0 0.4 - - - -
108B ALA* 3.9 26.2 - - + -
109B GLY* 4.0 6.3 - - - -
112B ALA* 4.4 3.1 - - + -
141B ARG* 3.2 52.9 - - + -
187B PHE* 3.9 23.3 - + - -
188B GLY 3.4 11.7 + - - +
189B VAL* 3.2 21.5 - - - +
190B TYR 4.4 2.5 + - - +
191B ALA* 4.0 5.5 - - - -
194B GLY 5.8 0.2 + - - -
214B CYS* 1.3 85.9 - - - +
216B ASP* 1.3 73.5 + - - +
221B ILE* 3.1 19.6 - - - +
233B THR* 3.1 6.1 - - - -
234B MET* 3.8 28.3 - - + -
236B GLN* 4.9 7.4 - - + -
281B VAL* 5.4 2.0 - - + -
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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