Contacts of the strand formed by residues 180 - 187 (chain B) in PDB entry 3SRF
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 ILE 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B LEU* 4.3 13.5 - - + -
173B ILE 3.7 0.5 - - - +
174B TYR* 3.3 8.8 - - - -
175B VAL* 2.8 55.8 + - + +
176B ASP* 4.7 9.9 - - + +
179B LEU* 1.3 84.7 - - + +
181B SER* 1.3 62.1 + - - +
182B LEU* 4.0 23.6 - - + -
196B VAL* 5.0 1.1 - - + -
198B ASN 3.7 14.4 - - - +
199B GLY* 4.5 5.2 - - - +
200B GLY* 3.6 26.7 - - - +
201B SER 4.2 13.2 - - - +
202B LEU* 4.2 16.8 - - + -
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Residues in contact with SER 181 (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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172B LYS* 4.5 7.3 - - - +
173B ILE 3.5 4.5 + - - -
174B TYR* 3.7 29.9 + - - -
180B ILE* 1.3 76.3 - - - +
182B LEU* 1.3 73.0 + - - +
196B VAL 3.8 0.2 - - - -
197B GLU* 2.9 40.0 + - - +
198B ASN* 2.9 27.3 + - - -
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Residues in contact with LEU 182 (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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133B LEU* 4.2 0.4 - - + -
139B LEU* 3.8 32.5 - - + -
141B ILE* 4.2 16.8 - - + -
156B LEU* 4.7 1.8 - - + -
171B SER 3.8 0.7 - - - +
172B LYS* 3.4 4.5 - - - +
173B ILE* 2.7 51.0 + - + +
175B VAL* 4.0 23.1 - - + -
180B ILE* 4.0 16.8 - - + -
181B SER* 1.3 86.9 + - - +
183B GLN* 1.3 60.8 + - - +
194B THR* 3.9 19.7 - - - +
195B GLU 3.4 4.3 - - - -
196B VAL* 3.9 22.9 - - + -
197B GLU* 4.8 0.2 - - - -
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Residues in contact with GLN 183 (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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170B GLY* 3.3 34.0 + - - +
171B SER 3.7 3.1 - - - +
172B LYS* 3.4 25.9 + - + +
182B LEU* 1.3 73.4 - - - +
184B VAL* 1.3 68.6 + - - +
185B LYS* 3.5 19.6 + - - +
194B THR* 3.3 2.7 - - - -
195B GLU* 2.9 38.9 + - + +
197B GLU* 3.2 32.0 - - + +
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Residues in contact with VAL 184 (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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167B VAL* 4.3 12.1 - - + -
168B GLU 3.3 27.8 - - - +
169B VAL* 3.8 10.5 - - - +
170B GLY* 2.8 26.6 + - - +
171B SER 3.1 18.1 + - - +
173B ILE* 3.8 26.7 - - + -
183B GLN* 1.3 71.7 - - - +
185B LYS* 1.3 71.2 + - - +
186B GLN 4.2 16.8 - - - +
187B LYS* 4.8 3.1 - - + -
192B LEU* 4.6 13.9 - - + -
193B VAL 3.9 4.7 - - - +
194B THR* 4.3 5.4 - - + -
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Residues in contact with LYS 185 (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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169B VAL* 3.3 28.4 - - - +
170B GLY* 5.7 1.5 - - - -
183B GLN* 3.6 30.4 + - - +
184B VAL* 1.3 88.0 - - - +
186B GLN* 1.3 72.0 + - - +
193B VAL* 2.8 19.7 + - + +
194B THR 4.5 1.6 - - - -
195B GLU* 3.6 33.0 + - + +
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Residues in contact with GLN 186 (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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184B VAL* 4.2 5.4 - - - +
185B LYS* 1.3 89.8 - - - +
187B LYS* 1.3 63.5 + - - +
191B PHE* 5.6 2.0 - - + -
192B LEU* 3.9 1.7 - - - -
193B VAL* 2.9 55.7 + - + +
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Residues in contact with LYS 187 (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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164B CYS* 3.2 20.0 + - + +
165B LYS* 5.2 2.6 + - - +
167B VAL* 3.0 29.7 + - + -
168B GLU* 3.5 23.0 + - - +
169B VAL* 4.7 15.9 - - + +
184B VAL* 4.8 3.8 - - + -
185B LYS 4.0 1.8 + - - -
186B GLN* 1.3 76.5 - - - +
188B GLY* 1.3 73.7 + - - +
191B PHE* 5.3 0.7 - - - -
192B LEU* 3.6 23.3 - - + -
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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