Contacts of the strand formed by residues 187 - 190 (chain D) in PDB entry 1G82
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 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D LEU* 3.8 25.6 - - + -
67D TYR 3.3 3.4 - - - -
68D CYS* 3.6 36.3 - - + -
74D LEU* 4.4 12.1 - - + -
145D TYR* 3.3 6.9 - - - -
146D ASN* 2.7 39.7 + - - +
148D TYR* 3.8 23.7 - + + -
164D VAL* 3.3 42.4 - - + -
165D ALA* 3.9 7.6 - - - -
166D LEU* 3.9 17.5 - - + -
184D PHE 3.7 9.4 - - - -
185D THR 3.0 22.2 - - - -
186D HIS* 1.4 72.5 - - - +
188D LEU* 1.3 58.8 + - - +
189D PRO* 3.4 7.5 - - - +
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Residues in contact with LEU 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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143A ASN 4.7 3.6 - - - +
145A TYR* 6.2 0.9 - - + -
188A LEU* 3.7 45.1 - - + -
190A ARG* 4.9 2.2 - - - -
65D GLN 3.3 0.2 - - - +
66D LEU* 3.4 3.0 - - - -
67D TYR* 2.8 45.9 + - + +
143D ASN 4.1 2.0 - - - +
144D TRP* 3.2 32.5 - - + +
145D TYR* 3.4 30.0 - - + +
187D PHE* 1.3 72.2 - - - +
189D PRO* 1.3 75.8 - - + +
190D ARG* 3.3 15.4 + - + -
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Residues in contact with PRO 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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190A ARG* 5.2 4.5 + - - +
191A PRO* 3.6 18.1 - - + +
64D ARG* 3.8 23.8 - - + -
65D GLN 3.5 6.7 - - - +
66D LEU* 3.7 8.7 - - + -
97D PHE* 4.9 3.8 - - + -
138D GLU* 4.8 2.2 - - - +
144D TRP 3.6 14.6 - - - +
146D ASN* 3.5 9.6 - - - +
148D TYR* 3.5 22.7 - - - +
187D PHE 3.4 9.9 - - - +
188D LEU* 1.3 92.2 - - + +
190D ARG* 1.3 58.8 + - - +
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Residues in contact with ARG 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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144A TRP* 3.4 50.9 + - + +
188A LEU* 5.1 5.1 - - + +
189A PRO* 4.9 3.8 + - - +
191A PRO* 4.3 0.9 - - - -
64D ARG* 3.3 9.6 - - - +
65D GLN* 2.7 45.4 + - + +
67D TYR* 3.8 10.1 - - + -
73D HIS* 3.0 31.9 + - - -
88D ASP* 2.8 28.5 + - - -
89D HIS* 5.3 2.8 - - - -
188D LEU* 3.8 25.6 - - + +
189D PRO* 1.3 74.0 - - - +
191D PRO* 1.3 76.1 + - + +
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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