Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 4GB1
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 SER 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.1 1.8 - - - -
179A ALA* 3.2 4.7 + - - +
180A TRP* 1.3 96.8 - - - +
182A ALA* 1.3 60.9 + - - +
196A VAL* 3.0 36.5 + - - +
226A ARG* 3.8 3.8 - - - +
227A THR* 3.3 21.7 + - - -
229A GLU* 2.4 32.8 + - - -
501A 0LP 4.1 8.1 - - - -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 4.2 6.8 - - + -
134A LEU* 4.1 11.9 - - + -
158A LEU* 3.7 41.7 - - + -
179A ALA* 4.3 1.6 - - + -
181A SER* 1.3 76.4 + - - +
183A THR* 1.3 60.4 + - - +
194A VAL 3.3 6.1 - - - +
227A THR* 3.4 6.2 - - - +
229A GLU* 2.8 43.2 + - - +
230A SER 4.1 0.2 + - - -
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 4.2 3.8 - - - -
158A LEU* 4.6 0.9 - - - +
182A ALA* 1.3 75.8 - - - +
184A ALA* 1.3 59.9 + - - +
193A THR* 3.4 2.1 - - - -
194A VAL* 2.8 60.3 + - + +
227A THR* 3.7 22.0 - - + +
228A GLN* 3.8 8.4 + - - -
230A SER 2.9 22.7 + - - -
232A CYS* 3.3 20.8 - - + +
241A TRP* 4.0 17.7 - - + -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 3.7 13.2 - - + -
123A SER* 3.6 6.1 - - - -
132A PHE* 3.6 41.1 - - + -
158A LEU* 4.9 1.1 - - + -
183A THR* 1.3 78.2 + - - +
185A CYS* 1.3 60.7 + - - +
191A TRP* 4.7 0.2 - - + -
192A MET 3.4 9.6 - - - +
193A THR* 4.0 7.9 - - + -
231A SER* 3.4 11.3 + - - -
232A CYS* 3.1 19.6 + - - -
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Residues in contact with CYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER* 3.7 7.9 - - - +
184A ALA* 1.3 72.8 - - - +
186A HIS* 1.3 60.5 + - - +
187A ASP 4.2 0.2 + - - -
190A LYS 4.2 0.2 - - - +
191A TRP* 3.5 6.2 - - - -
192A MET* 2.9 36.9 + - - +
231A SER* 4.0 1.6 - - - +
232A CYS* 2.0 60.8 - - - +
233A THR* 4.7 0.4 - - - -
234A CYS* 3.5 24.8 - - - +
239A CYS* 3.8 11.7 - - - -
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Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 3.2 19.2 - - - +
123A SER* 4.2 2.6 + - - -
124A CYS 3.8 15.2 + - - +
125A SER* 3.1 23.9 - - - -
126A PRO* 3.5 12.5 - - + +
127A ILE* 6.5 0.9 - - + -
185A CYS* 1.3 75.6 - - - +
187A ASP* 1.3 61.5 + - - +
188A GLY 2.9 36.5 + - - -
189A LYS 3.3 24.8 + - - -
190A LYS* 3.2 19.5 - - - -
191A TRP* 3.2 37.4 + + + -
234A CYS* 3.5 9.5 - - - +
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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