Contacts of the strand formed by residues 183 - 189 (chain a) in PDB entry 5GJQ
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 GLY 183 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40a ARG* 3.2 20.6 - - - -
178a ALA 3.6 4.2 - - - +
179a ILE* 3.7 0.3 - - - -
180a ALA* 3.1 27.5 + - - +
182a SER* 1.3 81.2 - - - +
184a VAL* 1.3 66.5 + - - -
185a GLU* 4.0 8.4 + - - +
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Residues in contact with VAL 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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39a ASP 3.6 23.8 - - - +
40a ARG* 4.4 4.3 - - + +
42a PHE* 3.7 36.3 - - + -
177a ALA* 4.6 5.4 - - + -
178a ALA 3.4 7.0 - - - +
179a ILE* 4.2 17.9 - - + -
183a GLY* 1.3 78.5 - - - +
185a GLU* 1.3 63.6 + - - +
186a ARG* 3.9 19.9 + - + +
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Residues in contact with GLU 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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149a LYS* 2.4 39.3 + - - +
153a LEU* 5.8 0.3 - - - +
177a ALA* 3.3 2.8 - - - -
178a ALA* 2.9 39.7 + - + +
180a ALA* 5.8 2.8 - - - +
182a SER* 4.7 14.4 - - - -
183a GLY 4.4 7.0 - - - +
184a VAL* 1.3 76.9 - - - +
186a ARG* 1.3 61.2 + - - +
187a GLN* 4.0 10.0 + - - +
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Residues in contact with ARG 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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32a ASP* 2.9 39.1 + - - -
34a LEU* 3.5 26.9 + - - +
36a PRO* 4.4 9.3 - - - +
42a PHE* 3.8 25.9 - - - -
175a ARG* 4.4 9.8 - - - +
176a LEU 3.5 7.2 + - - +
177a ALA* 4.1 9.3 - - + +
184a VAL* 3.9 19.8 + - + +
185a GLU* 1.3 74.2 - - - +
187a GLN* 1.3 63.0 + - - +
188a VAL* 5.6 1.3 - - + -
215u ILE* 5.8 2.9 - - - -
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Residues in contact with GLN 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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153a LEU* 3.4 35.6 - - - +
175a ARG* 3.7 2.4 - - - +
176a LEU* 2.9 59.7 + - + +
178a ALA* 5.9 1.4 - - - +
185a GLU* 4.9 9.8 + - - +
186a ARG* 1.3 75.8 - - - +
188a VAL* 1.3 69.0 + - - +
189a LEU* 3.9 18.6 - - + +
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Residues in contact with VAL 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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173a VAL* 3.5 26.0 - - + -
174a ILE 3.5 6.5 - - - +
175a ARG* 3.6 31.9 - - + +
186a ARG* 5.6 1.3 - - + -
187a GLN* 1.3 84.6 - - - +
189a LEU* 1.3 65.5 + - - +
190a LEU* 3.7 16.7 + - + +
193a GLN* 3.5 15.1 + - - +
212u ALA* 4.5 3.1 - - + -
213u HIS* 3.4 31.4 + - + +
215u ILE* 5.7 1.1 - - + -
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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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154a GLN* 5.9 0.4 - - - +
157a ALA* 3.6 32.3 - - + -
173a VAL* 3.2 1.3 - - - +
174a ILE* 2.9 45.7 + - + +
176a LEU* 3.7 20.6 - - + -
187a GLN* 3.9 19.1 - - + +
188a VAL* 1.3 74.3 - - - +
190a LEU* 1.3 59.0 + - - +
193a GLN* 3.7 34.8 - - + +
194a ILE* 3.4 17.2 - - + +
195a PRO* 4.8 2.5 - - + -
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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