Contacts of the strand formed by residues 186 - 192 (chain A) in PDB entry 1GM5
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 ASN 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR* 5.2 2.6 + - - +
180A LYS 2.8 9.4 - - - +
181A LYS* 3.2 31.2 - - - +
185A MET* 1.3 96.4 - - - +
187A ILE* 1.3 77.0 + - - +
204A PHE 3.6 12.2 - - - +
205A ASN* 3.8 15.0 + - - +
206A GLN 5.4 3.8 - - - +
207A ASP* 5.4 12.9 + - + +
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Residues in contact with ILE 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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179A THR* 2.7 13.4 - - - -
180A LYS* 2.2 86.5 + - + +
182A PHE* 3.9 14.4 - - + -
185A MET* 4.4 11.0 - - + -
186A ASN* 1.3 86.3 - - - +
188A LEU* 1.3 60.2 + - - +
189A THR* 4.3 9.9 - - + -
202A LYS* 4.7 5.4 - - + -
203A TRP 3.2 11.4 - - - +
204A PHE* 4.1 3.1 - - + -
11X A 3.2 54.7 - - + +
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Residues in contact with LEU 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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177A VAL* 4.2 11.7 - - + -
178A GLU 3.4 9.4 - - - +
179A THR* 4.0 7.0 - - + +
187A ILE* 1.3 73.8 - - - +
189A THR* 1.3 67.1 + - - +
201A LEU 4.1 0.2 - - - +
203A TRP* 2.5 60.9 + - + +
204A PHE 4.3 0.6 + - - -
206A GLN 3.8 13.2 - - - +
207A ASP* 3.9 5.2 - - - +
209A LEU* 2.9 38.1 - - + -
210A GLN* 3.6 23.3 - - + +
213A LEU* 3.0 25.4 - - + -
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Residues in contact with THR 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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176A SER 2.5 7.5 - - - +
177A VAL* 2.9 3.0 - - - +
178A GLU* 2.3 84.8 + - - +
180A LYS* 4.4 11.1 - - - +
187A ILE* 4.3 4.3 - - + -
188A LEU* 1.3 76.2 - - - +
190A ALA* 1.3 54.6 + - - +
191A VAL* 5.0 3.4 - - + -
201A LEU 3.4 5.8 - - - +
202A LYS* 2.7 54.7 - - + -
203A TRP* 5.2 0.2 - - - -
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Residues in contact with ALA 190 (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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174A ILE* 5.3 11.0 - - + -
176A SER 1.9 32.5 - - - +
177A VAL* 3.8 15.7 - - + -
189A THR* 1.3 65.5 - - - +
191A VAL* 1.3 70.1 + - - +
201A LEU* 3.0 29.1 + - + +
203A TRP* 4.9 10.7 - - + -
213A LEU* 4.5 12.1 - - + -
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Residues in contact with VAL 191 (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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174A ILE* 3.1 3.3 - - - -
175A VAL* 2.6 35.4 + - - +
176A SER* 2.5 29.2 + - - +
178A GLU* 4.9 7.0 - - - +
189A THR* 5.0 3.1 - - - -
190A ALA* 1.3 90.4 - - - +
192A LEU* 1.3 70.7 + - - +
193A SER* 5.4 0.2 - - - -
198A HIS* 4.1 11.0 - - + +
199A VAL 2.2 57.4 - - - +
200A PRO* 3.0 22.7 - - + -
201A LEU* 4.0 3.1 - - - +
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Residues in contact with LEU 192 (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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159A LEU* 4.0 13.9 - - + +
170A THR* 3.8 23.3 - - + -
171A GLN 3.8 21.8 - - - +
172A GLY* 3.5 14.4 - - - +
173A LYS 2.5 31.0 - - - +
174A ILE* 3.8 10.8 - - + -
191A VAL* 1.3 77.8 - - - +
193A SER* 1.3 60.3 + - - +
194A ASP 4.0 1.5 + - - -
198A HIS* 3.3 5.0 - - - +
199A VAL* 3.1 30.6 + - + +
201A LEU* 4.1 22.4 - - + -
221A VAL* 5.1 1.8 - - + +
223A VAL* 4.2 20.2 - - + -
238A ILE* 5.6 0.2 - - + -
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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