Contacts of the strand formed by residues 190 - 197 (chain B) in PDB entry 5H4Z
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 VAL 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.9 29.4 - - + -
198A PHE* 4.5 18.4 - - + -
152B LEU* 3.6 3.4 - - - -
153B LEU* 2.9 44.1 + - + +
188B GLY 4.1 2.0 - - - +
189B ARG* 1.3 80.0 - - - +
191B LEU* 1.3 65.0 + - - +
192B VAL* 3.8 17.7 + - + -
211B ARG* 4.3 16.6 - - + +
212B VAL 3.4 8.3 - - - +
213B PRO* 4.0 10.5 - - + -
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Residues in contact with LEU 191 (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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116B LEU* 3.7 35.7 - - + -
125B LEU* 5.2 0.9 - - + -
127B VAL* 3.9 25.1 - - + -
150B VAL* 3.8 23.8 - - + -
151B TYR 3.3 21.1 - - - +
152B LEU* 3.8 10.8 - - + +
179B PHE* 4.3 4.5 - - + -
190B VAL* 1.3 72.5 - - - +
192B VAL* 1.3 60.4 + - - +
193B MET* 4.0 19.7 - - + -
210B VAL 3.5 2.3 - - - +
211B ARG* 3.3 5.4 - - - -
212B VAL* 2.9 37.8 + - + +
214B MET* 4.3 15.0 - - - -
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Residues in contact with VAL 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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149B ARG 3.5 1.0 - - - +
150B VAL* 3.3 7.3 - - - +
151B TYR* 2.8 67.1 + - + +
153B LEU* 3.6 31.0 - - + -
190B VAL* 4.0 9.0 - - + +
191B LEU* 1.3 78.1 - - - +
193B MET* 1.3 66.5 + - - +
194B ALA* 4.4 7.2 - - + +
209B GLU* 3.8 22.4 - - - +
210B VAL 3.6 2.9 - - - +
211B ARG* 3.9 17.7 - - + +
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Residues in contact with MET 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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112B LEU* 4.0 16.0 - - + +
114B TYR* 3.9 32.3 - - + -
127B VAL* 4.4 1.6 - - - -
129B ILE* 3.7 29.4 - - + -
148B VAL* 4.1 8.5 - - + -
149B ARG 3.5 4.5 - - - -
150B VAL* 4.3 7.0 - - + -
191B LEU* 4.0 22.4 - - + -
192B VAL* 1.3 78.4 - - - +
194B ALA* 1.3 60.5 + - - +
195B VAL* 3.9 4.9 + - - +
209B GLU* 3.4 3.8 - - - -
210B VAL* 3.0 59.7 + - + +
212B VAL* 3.9 17.9 - - + -
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Residues in contact with ALA 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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148B VAL* 3.2 3.4 - - - +
149B ARG* 2.8 45.0 + - + +
151B TYR* 5.5 2.5 - - + +
192B VAL* 3.9 6.7 - - + -
193B MET* 1.3 71.4 - - - +
195B VAL* 1.3 63.2 + - - +
196B TYR* 3.5 28.7 - - + +
208B GLY 3.8 5.2 - - - +
209B GLU* 3.9 17.0 - - + +
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Residues in contact with VAL 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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112B LEU* 4.7 9.9 - - + -
132B ALA* 5.5 3.4 - - + -
135B LEU* 4.3 14.8 - - + -
146B PRO* 4.4 12.8 - - + -
147B TYR 3.4 9.2 - - - +
148B VAL* 4.1 20.0 - - + +
173B PHE* 5.3 1.3 - - + -
193B MET 4.5 4.5 - - - +
194B ALA* 1.3 75.8 - - - +
196B TYR* 1.3 66.3 + - - +
206B ALA* 3.9 1.4 - - - +
207B ILE* 2.9 41.0 + - + -
208B GLY 2.8 15.6 + - - +
229B LEU* 3.9 32.3 - - + -
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Residues in contact with TYR 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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146B PRO* 3.1 6.9 - - - +
147B TYR* 2.8 77.0 + + + +
149B ARG* 4.1 24.3 - - + -
194B ALA* 3.5 37.0 - - + +
195B VAL* 1.3 73.4 - - - +
197B ASP* 1.3 60.1 + - - +
203B ARG* 6.1 2.2 - - - -
204B ASN* 4.6 9.9 - - + -
205B ASP 3.5 6.3 - - - -
206B ALA* 3.6 33.9 - - + +
207B ILE* 4.1 5.8 - - - +
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Residues in contact with ASP 197 (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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138B LEU* 3.0 21.8 - - + +
139B ASP* 2.9 5.6 - - - +
144B SER* 3.6 8.6 - - - +
145B ASP 2.9 25.8 + - - +
147B TYR* 4.3 0.2 - - - -
196B TYR* 1.3 70.7 - - - +
198B PHE* 1.3 61.1 + - - +
199B ASP* 3.1 2.6 - - - +
204B ASN* 3.3 7.2 - - - +
205B ASP* 2.7 44.0 + - + +
207B ILE* 4.0 5.5 - - + +
301B CA 2.5 20.4 - - - -
302B CA 2.3 31.0 - - - -
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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