Contacts of the strand formed by residues 185 - 191 (chain c) 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 VAL 185 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24c ALA 3.6 10.1 - - - +
25c ASP* 4.9 1.8 - - - -
26c ARG* 4.2 3.3 - - - -
171c MET* 4.0 31.9 - - + -
172c LEU* 3.7 28.0 - - + -
175c VAL* 4.7 15.9 - - + -
182c GLY* 5.2 0.2 - - - -
184c GLY* 1.3 82.7 - - - +
186c ILE* 1.3 69.9 + - - +
187c VAL* 4.2 3.6 - - + -
199c THR* 3.3 6.6 - - - -
200c LEU* 3.0 53.3 + - + -
202c ALA* 4.4 5.4 - - + +
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Residues in contact with ILE 186 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22c ILE 4.1 0.5 - - - +
23c ALA* 3.2 4.0 - - - +
24c ALA* 2.9 49.6 + - + +
25c ASP 4.9 1.8 - - - +
26c ARG* 3.9 37.2 - - + +
42c ILE* 4.6 6.5 - - + +
185c VAL* 1.3 75.5 - - - +
187c VAL* 1.3 65.3 + - - +
188c HIS* 3.9 18.4 - - + +
197c THR* 3.9 25.1 - - + -
198c ARG 3.4 12.1 - - - +
199c THR* 4.2 9.9 - - + -
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Residues in contact with VAL 187 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21c ALA* 4.9 2.0 - - + -
22c ILE 3.6 7.6 - - - +
23c ALA* 3.9 12.3 - - + -
164c PHE* 4.7 12.6 - - + -
167c ILE* 3.6 30.5 - - + -
168c SER* 4.0 8.7 - - - +
185c VAL* 4.2 2.7 - - + -
186c ILE* 1.3 79.3 - - - +
188c HIS* 1.3 70.2 + - - +
189c ILE* 3.9 4.4 + - + +
196c THR 3.5 1.6 - - - +
197c THR* 3.4 3.3 - - - -
198c ARG* 2.9 34.5 + - - +
200c LEU* 3.8 37.0 - - + -
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Residues in contact with HIS 188 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21c ALA* 3.3 2.4 - - - +
22c ILE* 2.9 45.9 + - + +
42c ILE* 3.8 36.0 + - + +
50c TYR* 3.7 27.3 - + + -
186c ILE* 3.9 18.1 - - + +
187c VAL* 1.3 75.4 - - - +
189c ILE* 1.3 62.2 + - - +
190c ILE* 4.0 10.9 + - + +
195c ILE* 4.7 2.9 - - + +
196c THR 3.2 5.1 + - - +
197c THR* 2.7 42.6 + - + -
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Residues in contact with ILE 189 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19c CYS* 4.0 18.2 - - + -
20c VAL 3.3 18.6 - - - +
21c ALA* 4.1 6.3 - - + +
160c PRO* 4.7 16.2 - - + +
163c LEU* 3.5 28.0 - - + -
164c PHE* 4.7 13.0 - - + -
187c VAL* 4.8 5.8 - - + +
188c HIS* 1.3 76.4 - - - +
190c ILE* 1.3 62.7 + - - +
191c GLU* 4.3 11.2 + - + +
195c ILE* 3.7 0.5 - - - -
196c THR* 2.9 51.4 + - - +
198c ARG* 4.0 17.9 - - + +
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Residues in contact with ILE 190 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19c CYS* 3.4 2.1 - - - +
20c VAL* 2.8 60.4 + - + +
22c ILE* 6.2 0.7 - - + -
48c ARG* 3.6 38.4 - - - +
49c LEU* 4.1 2.5 - - - +
50c TYR* 4.9 11.2 - - + +
110c ALA* 4.4 4.0 - - + +
111c GLY* 4.1 6.1 - - - -
112c LEU* 3.8 10.9 - - + +
188c HIS* 4.5 12.8 - - + +
189c ILE* 1.3 79.6 - - - +
191c GLU* 1.3 63.5 + - - +
194c LYS 3.8 2.2 - - - -
195c ILE* 3.7 34.3 - - + -
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Residues in contact with GLU 191 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219b LEU* 3.6 6.8 - - - +
18c ASN 4.3 3.6 - - - +
19c CYS* 4.1 14.8 - - + +
48c ARG* 5.2 1.6 - - - +
112c LEU* 3.5 12.9 - - - +
160c PRO* 3.3 36.8 - - - +
189c ILE* 4.6 9.7 - - + +
190c ILE* 1.3 81.3 - - - +
192c LYS* 1.3 68.3 + - - +
193c ASP* 3.2 9.4 - - - +
194c LYS* 2.8 56.7 + - + +
196c THR* 4.5 5.6 + - - +
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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