Contacts of the strand formed by residues 191 - 196 (chain B) in PDB entry 3V3H
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 TYR 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.6 15.5 - - + +
45B LYS 2.8 26.6 + - - -
46B PRO* 5.0 1.1 - - + -
47B LEU* 3.9 20.6 - - + -
82B GLY* 3.1 20.0 - - - -
83B PRO* 3.7 9.4 - - + +
189B LEU 3.2 20.0 - - - +
190B ASP* 1.3 76.4 - - - +
192B TRP* 1.3 75.1 + - - +
193B THR* 3.9 21.1 - - + -
210B ILE* 3.9 20.6 - - + -
211B VAL 3.3 12.8 - - - +
212B LEU* 4.0 4.7 - - + -
213B LYS 4.2 1.8 - - - +
258B ALA* 3.5 2.4 - - - -
259B SER* 2.9 54.6 + - - -
260B PHE* 3.6 6.7 - - - -
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Residues in contact with TRP 192 (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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33B ILE* 3.6 39.9 - - + +
35B THR* 3.9 24.1 - - + +
38B ALA* 4.0 15.5 - - + +
109B VAL* 4.0 30.1 - - + -
147B PHE* 4.3 3.1 - + - -
191B TYR* 1.3 76.1 - - - +
193B THR* 1.3 60.6 + - - +
194B TYR* 5.6 1.3 - - + -
209B TRP 3.8 0.3 - - - +
210B ILE* 3.4 3.3 - - - -
211B VAL* 2.8 52.9 + - + +
212B LEU 3.8 5.4 - - - -
213B LYS* 3.4 40.4 - - + -
256B ILE* 3.7 11.9 - - + -
257B LYS 3.1 7.9 - - - +
258B ALA* 3.7 22.2 - - + +
260B PHE* 3.6 25.7 - + - -
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Residues in contact with THR 193 (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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44B LEU* 4.2 4.5 - - + -
83B PRO* 3.5 26.6 - - + +
191B TYR* 3.9 24.7 - - + -
192B TRP* 1.3 75.3 - - - +
194B TYR* 1.3 67.7 + - - +
208B THR* 3.7 7.4 - - - +
209B TRP 2.8 18.8 + - - -
210B ILE* 4.6 0.4 - - - -
255B GLN 3.9 1.4 - - - +
256B ILE* 3.6 1.7 - - - -
257B LYS* 2.9 60.4 + - - +
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Residues in contact with TYR 194 (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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29B SER* 2.8 28.6 + - - -
30B PRO* 3.7 3.5 - - - +
31B VAL* 3.5 24.6 - - + +
33B ILE* 5.8 2.9 - - + -
107B HIS* 2.7 36.0 + + - -
192B TRP 5.6 0.7 - - - -
193B THR* 1.3 85.1 + - - +
195B PRO* 1.3 90.7 - - + +
196B GLY* 4.0 2.2 - - - -
208B THR* 3.9 2.2 - - - -
209B TRP* 2.9 45.4 + + + +
211B VAL* 4.8 4.9 - - + -
251B LEU* 5.0 2.5 - - + -
254B ARG* 3.4 26.9 - - + -
255B GLN 4.0 11.2 - - - +
256B ILE* 4.0 19.1 - - + -
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Residues in contact with PRO 195 (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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27B ARG* 4.0 19.6 - - - +
138B PRO 6.2 0.2 - - - +
194B TYR* 1.3 89.0 - - + +
196B GLY* 1.3 58.0 + - - +
207B VAL 3.7 6.1 - - - +
208B THR* 4.7 4.5 - - - +
254B ARG* 2.8 48.8 + - + -
255B GLN 4.4 8.7 - - - +
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Residues in contact with GLY 196 (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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27B ARG* 3.2 19.8 + - - +
29B SER* 3.3 11.9 - - - -
194B TYR* 3.6 2.8 + - - -
195B PRO* 1.3 75.5 - - - +
197B SER* 1.3 58.5 + - - -
205B GLU* 3.5 7.1 - - - +
206B CYS 3.4 6.2 + - - -
207B VAL* 2.8 33.9 + - - -
209B TRP* 3.8 3.8 - - - -
254B ARG* 3.6 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