Contacts of the strand formed by residues 202 - 211 (chain B) in PDB entry 3RHW
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 CYS 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B PRO* 4.7 4.0 - - - -
147B ASP* 4.3 6.5 - - - -
148B LEU 3.3 20.4 - - - -
149B ALA* 3.5 11.7 - - + -
160B TYR* 4.9 1.1 - - - -
190B TYR* 3.4 8.3 - - - +
191B CYS* 2.0 78.4 + - - +
192B THR* 3.1 8.9 + - - +
193B SER* 6.0 0.4 - - - +
200B TYR 4.3 2.5 - - - +
201B SER* 1.3 81.6 + - - +
203B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 203 (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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32B VAL* 3.4 43.3 - - + -
147B ASP* 3.5 0.7 - - - -
148B LEU* 2.8 41.2 + - + +
160B TYR* 3.5 27.6 - - + -
161B LEU 3.8 3.6 - - - +
162B TRP* 3.4 32.8 - - + +
189B THR 3.5 3.4 - - - -
190B TYR* 3.3 37.2 - - + -
191B CYS* 3.2 10.3 - - - -
202B CYS* 1.3 73.9 - - - +
204B ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 3.9 15.3 - - - -
146B ILE 3.4 5.2 - - - -
147B ASP* 2.8 39.1 + - - +
162B TRP* 3.7 4.0 - - - -
187B SER 4.0 0.3 - - - +
188B THR* 3.8 0.3 - - - -
189B THR* 2.7 49.7 + - - +
190B TYR 5.6 1.2 + - - -
191B CYS* 3.9 30.4 - - + +
203B LEU* 1.3 75.2 - - - +
205B THR* 1.3 69.4 + - - +
206B THR* 3.8 9.1 + - - +
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Residues in contact with THR 205 (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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34B MET* 3.5 22.2 - - - -
36B LEU* 5.4 0.6 - - + +
145B SER* 3.1 6.8 - - - -
146B ILE* 2.9 60.6 + - + +
162B TRP* 3.7 17.3 - - + -
168B LEU* 3.3 33.4 - - + +
187B SER 3.4 6.0 + - - -
188B THR* 5.2 0.9 - - - -
204B ARG* 1.3 72.4 - - - +
206B THR* 1.3 64.2 + - - +
207B ILE* 5.0 2.8 - - - +
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Residues in contact with THR 206 (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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143B GLN* 4.1 26.0 - - + +
144B CYS 3.4 11.9 - - - +
145B SER* 3.1 17.8 + - - +
186B THR* 3.1 6.2 - - - -
187B SER* 2.8 55.7 + - - +
189B THR* 5.0 1.7 + - - -
204B ARG* 3.8 13.0 + - - +
205B THR* 1.3 75.1 + - - +
207B ILE* 1.3 73.7 + - - +
208B GLN* 5.9 0.2 - - + -
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Residues in contact with ILE 207 (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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36B LEU* 3.8 24.5 - - + -
39B ILE* 3.2 36.6 - - + -
49B TYR* 4.3 14.1 - - + +
143B GLN* 3.4 3.6 - - - -
144B CYS* 2.8 45.9 + - + +
146B ILE* 6.4 0.4 - - + -
168B LEU* 4.9 3.4 - - + -
183B LEU* 4.0 11.9 - - + -
185B ASN 3.5 3.4 - - - -
186B THR* 3.8 16.4 - - + -
205B THR* 5.0 2.2 - - + +
206B THR* 1.3 79.9 - - - +
208B GLN* 1.3 60.4 + - - +
209B LEU* 4.0 22.9 + - + +
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Residues in contact with GLN 208 (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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141B VAL* 4.3 27.2 - - + +
142B GLN 3.5 9.2 - - - +
143B GLN* 3.0 30.7 + - + +
183B LEU* 3.6 3.7 - - - +
184B THR* 3.0 46.8 + - - +
185B ASN* 2.7 34.5 + - + +
206B THR* 5.9 0.4 - - + -
207B ILE* 1.3 74.0 - - - +
209B LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 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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39B ILE* 5.0 2.0 - - + -
42B ILE* 3.4 29.6 - - + -
49B TYR* 5.7 0.9 - - + -
141B VAL* 3.3 7.6 - - - -
142B GLN* 2.8 46.1 + - + +
144B CYS* 4.1 24.0 - - + -
178B LEU* 4.0 26.9 - - + -
181B PHE* 3.9 20.7 - - + -
182B GLN 3.9 1.1 - - - -
183B LEU* 4.1 19.7 - - + -
207B ILE* 4.1 23.6 - - + +
208B GLN* 1.3 76.0 - - - +
210B LYS* 1.3 60.3 + - - +
211B ARG 3.9 1.1 + - - -
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Residues in contact with LYS 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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140B ASP 4.7 0.9 - - - +
141B VAL* 3.6 22.4 - - + -
181B PHE* 3.4 2.7 - - - -
182B GLN* 2.9 49.6 + - + +
184B THR* 3.6 28.5 - - + -
208B GLN 3.9 0.8 + - - -
209B LEU* 1.3 71.5 - - - +
211B ARG* 1.3 71.9 + - - +
212B GLU* 3.4 0.3 + - - -
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Residues in contact with ARG 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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44B VAL* 3.9 24.9 - - - +
132B MET* 5.4 1.0 - - - -
134B LEU* 4.4 4.9 - - - +
137B TYR* 3.4 22.9 + - - -
138B PRO 3.7 14.2 - - - +
139B MET* 5.5 2.9 - - - -
140B ASP* 2.7 56.2 + - - +
142B GLN* 4.8 5.1 - - - +
180B SER 4.4 3.4 - - - +
181B PHE* 3.4 43.0 - - + -
209B LEU 3.9 0.4 + - - -
210B LYS* 1.3 79.5 - - - +
212B GLU* 1.3 67.9 + - - +
213B PHE* 3.5 4.9 + - - +
216B TYR* 3.4 43.3 + - + -
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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