Contacts of the strand formed by residues 187 - 195 (chain d) 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 187 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40d GLU* 3.5 18.8 - - - -
41d LYS* 5.4 0.7 - - - -
183d ILE* 3.4 4.0 - - - -
184d ASP* 3.2 21.6 + - - -
185d LYS 3.4 4.4 + - - -
186d ASN* 1.3 81.5 - - - +
188d ILE* 1.3 64.5 + - - -
189d HIS* 3.2 18.4 - - - -
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Residues in contact with ILE 188 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37d LYS* 4.1 19.7 - - + -
39d SER 3.9 14.8 - - - +
40d GLU* 3.5 14.2 + - - +
42d ILE 3.9 13.9 - - - +
43d LEU* 3.7 45.1 - - + -
181d ARG* 4.0 18.6 - - + -
182d ILE 3.5 7.0 - - - +
183d ILE* 4.1 14.4 - - + +
187d GLY* 1.3 73.6 - - - -
189d HIS* 1.3 65.0 + - - +
190d ASP* 4.3 6.3 + - - +
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Residues in contact with HIS 189 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153d ARG* 5.4 1.1 - - - -
181d ARG* 3.5 2.8 - - - +
182d ILE* 2.8 53.3 + - + +
184d ASP* 2.9 37.7 + - - -
186d ASN* 3.7 26.7 - - + +
187d GLY 3.2 20.8 + - - -
188d ILE* 1.3 74.6 + - - +
190d ASP* 1.3 65.8 - - - +
191d LEU* 4.6 5.4 - - + -
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Residues in contact with ASP 190 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37d LYS* 4.4 10.8 + - - -
180d VAL 4.2 3.4 - - - -
181d ARG* 2.9 36.6 + - - +
188d ILE* 4.4 6.2 - - - +
189d HIS* 1.3 77.2 - - - +
191d LEU* 1.3 67.5 + - - +
192d ASP* 4.2 1.2 + - - +
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Residues in contact with LEU 191 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14d LEU* 4.1 10.8 - - + -
157d VAL* 4.1 16.8 - - + -
180d VAL* 3.0 42.8 + - + +
181d ARG* 5.8 0.3 + - - -
182d ILE* 3.7 35.9 - - + -
189d HIS* 4.2 6.5 - - + +
190d ASP* 1.3 84.4 - - - +
192d ASP* 1.3 72.6 + - - +
193d ASN* 3.5 8.1 + - - +
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Residues in contact with ASP 192 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180d VAL* 4.2 7.8 - - - +
190d ASP 5.3 0.7 - - - +
191d LEU* 1.3 83.9 - - - +
193d ASN* 1.3 68.3 + - - +
194d ILE* 3.4 8.1 + - - +
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Residues in contact with ASN 193 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19d ARG* 3.6 34.4 + - - +
161d ARG* 5.6 1.4 + - - -
177d THR* 5.6 1.6 - - - -
178d PHE 3.5 18.3 - - - +
179d SER* 4.0 12.5 + - - -
180d VAL* 4.6 0.4 + - - -
191d LEU 4.0 6.1 - - - +
192d ASP* 1.3 77.9 - - - +
194d ILE* 1.3 65.0 + - - +
195d SER* 3.3 14.4 + - - -
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Residues in contact with ILE 194 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157d VAL* 4.6 11.7 - - + +
160d LEU* 4.5 4.9 - - + -
161d ARG* 3.5 56.1 - - + +
164d LEU* 3.7 28.7 - - + -
177d THR* 3.6 1.7 - - - -
178d PHE* 2.8 39.5 + - + +
180d VAL* 3.6 21.5 - - + -
192d ASP 3.4 5.8 + - - +
193d ASN* 1.3 69.7 - - - +
195d SER* 1.3 61.4 + - - +
196d PHE* 4.1 21.1 - - + -
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Residues in contact with SER 195 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161d ARG* 5.4 3.5 + - - +
176d PRO 3.5 4.7 - - - -
177d THR* 3.8 23.6 - - - -
193d ASN* 3.3 14.2 + - - +
194d ILE* 1.3 76.8 - - - +
196d PHE* 1.3 75.8 + - - +
197d PRO* 3.8 12.3 - - - +
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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