Contacts of the strand formed by residues 184 - 189 (chain A) in PDB entry 5GT8
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 PHE 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PRO* 5.2 2.9 - - + -
182A ASN* 3.8 38.1 - - + -
183A ARG* 1.3 73.9 - - - +
185A CYS* 1.3 60.8 + - - +
225A ILE* 4.6 5.6 - - + -
227A PHE* 3.6 35.9 - + + -
240A VAL* 4.1 11.7 - - + -
241A MET 3.1 21.8 - - - +
242A ASP* 4.3 8.3 - - - -
262A LEU* 3.8 3.3 - - - +
263A TRP* 3.0 39.8 + - - +
265A MET* 3.4 48.9 - - + -
307A LEU* 3.9 23.6 - - + -
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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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183A ARG 4.1 0.7 - - - -
184A PHE* 1.3 77.7 - - - +
186A VAL* 1.3 63.1 + - - +
187A LEU* 3.4 28.1 - - + +
240A VAL* 3.4 4.7 - - - +
241A MET 2.8 31.7 + - - +
243A ALA* 4.1 22.7 - - - -
246A GLN* 4.5 12.8 - - + +
256A THR* 5.1 2.2 - - - +
259A SER* 6.0 0.2 - - - -
262A LEU* 3.7 33.7 - - + -
263A TRP* 4.3 3.8 - - - -
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Residues in contact with VAL 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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118A TYR* 4.4 21.5 - - + +
185A CYS* 1.3 75.5 - - - +
187A LEU* 1.3 60.8 + - - +
238A SER* 5.0 2.2 - - - +
239A ILE 3.7 6.1 - - - +
240A VAL* 4.5 14.6 - - + +
255A LEU 4.0 0.2 - - - +
256A THR* 3.2 24.9 + - - -
257A SER* 4.3 3.9 + - - -
259A SER* 5.3 0.2 + - - -
263A TRP* 3.9 35.8 - - + +
296A TYR* 3.5 46.4 - - + +
307A LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 187 (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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118A TYR* 4.5 4.9 - - - +
185A CYS* 3.4 36.1 - - + +
186A VAL* 1.3 76.1 - - - +
188A THR* 1.3 60.7 + - - +
238A SER* 3.8 3.8 + - - -
239A ILE* 2.9 39.4 + - + +
241A MET* 3.9 23.8 - - + -
246A GLN* 4.1 19.3 - - + +
254A LEU* 3.9 35.2 - - + +
255A LEU 3.1 8.7 - - - +
256A THR* 3.5 28.9 - - - +
258B SER 5.0 0.7 - - - +
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Residues in contact with THR 188 (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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118A TYR* 3.6 46.3 - - + -
187A LEU* 1.3 75.3 - - - +
189A LEU* 1.3 76.1 + - - +
236A TYR* 5.9 2.8 - - - +
237A ILE* 2.7 23.8 + - - -
239A ILE* 5.7 0.9 - - - -
254A LEU* 3.8 5.0 - - - +
255A LEU* 2.8 52.7 + - + +
255B LEU* 4.1 4.0 - - + -
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Residues in contact with LEU 189 (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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188A THR* 1.3 90.6 + - - +
190A ASP* 1.3 72.1 + - - +
191A PRO* 3.3 9.7 - - - +
193A THR* 3.1 24.5 - - - +
194A LEU* 4.0 24.2 - - + -
197A ILE* 3.4 33.0 - - + -
237A ILE* 3.9 29.4 + - + +
239A ILE* 5.0 0.9 - - + -
253A LEU* 3.2 33.7 - - + +
254A LEU* 4.6 8.7 - - + +
255A LEU* 4.4 6.7 - - - -
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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