Contacts of the strand formed by residues 168 - 172 (chain G) in PDB entry 2W8B
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 ARG 168 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ILE* 3.7 18.5 - - + +
71G VAL 3.0 12.3 - - - +
72G TYR* 4.0 6.5 - - + -
73G PHE* 4.0 7.7 - - - -
107G GLY* 3.7 0.3 - - - -
108G HIS* 3.0 68.1 + - + +
109G ALA 5.5 0.2 + - - -
125G ARG* 4.7 1.1 - - - -
152G LYS* 2.9 24.2 + - - +
153G PRO* 3.8 3.4 + - - +
154G ALA* 3.5 33.0 - - - +
165G LYS 3.3 18.8 - - - -
166G ASN* 3.2 23.5 + - - +
167G ARG* 1.3 74.3 - - - +
169G ALA* 1.3 61.3 + - - +
170G VAL* 3.9 17.5 - - + +
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Residues in contact with ALA 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN 3.9 0.3 - - - +
70G ILE* 3.4 4.5 - - - -
71G VAL* 2.9 30.9 + - + +
73G PHE* 3.9 16.6 - - + -
105G VAL* 4.0 12.8 - - + -
106G GLU 3.2 6.1 - - - +
107G GLY* 4.2 0.9 - - - -
125G ARG* 4.3 10.8 - - + +
126G ALA 4.4 1.8 - - - +
129G VAL* 4.0 23.8 - - + -
168G ARG* 1.3 73.7 - - - +
170G VAL* 1.3 62.6 + - - +
171G LEU* 4.2 2.5 + - - +
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Residues in contact with VAL 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASN* 3.5 22.9 - - - +
70G ILE* 4.1 18.6 - - + -
104G THR 3.2 4.7 - - - +
105G VAL* 3.3 2.1 - - - -
106G GLU* 2.6 51.8 + - + +
108G HIS* 4.2 6.1 - - - +
168G ARG* 3.9 29.6 - - + +
169G ALA* 1.3 77.7 - - - +
171G LEU* 1.3 63.4 + - - +
172G VAL* 3.7 17.6 + - + -
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Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASN* 2.9 49.8 + - + +
71G VAL* 4.6 3.1 - - + -
87G MET* 4.1 9.4 - - + -
88G LEU* 4.0 26.9 - - + -
91G HIS* 3.7 37.5 - - + +
103G VAL* 3.8 15.5 - - + -
104G THR 3.6 4.3 - - - -
105G VAL* 4.6 4.3 - - + -
129G VAL* 4.1 15.5 - - + -
133G LEU* 4.2 17.9 - - + -
169G ALA 4.3 7.9 - - - +
170G VAL* 1.3 76.6 - - - +
172G VAL* 1.3 59.6 + - - +
173G TYR* 4.7 5.7 - - - -
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Residues in contact with VAL 172 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASN* 5.3 1.1 - - - +
103G VAL* 3.4 3.4 - - - +
104G THR* 2.7 39.7 + - - +
106G GLU* 3.7 31.6 - - + +
170G VAL* 3.8 21.8 - - + +
171G LEU* 1.3 78.6 - - - +
173G TYR* 1.3 66.0 + - - +
174G LEU* 3.2 31.3 + - + -
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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