Contacts of the strand formed by residues 103 - 107 (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 VAL 103 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 3.8 19.0 - - + +
101G TYR 4.3 0.2 - - - -
102G LYS* 1.3 76.2 - - - +
104G THR* 1.3 64.9 + - - +
105G VAL* 4.6 2.2 - - + -
133G LEU* 4.3 7.6 - - + -
142G GLN 3.0 15.9 + - - +
143G ILE* 3.5 18.6 - - + +
144G SER 3.2 21.7 + - - -
171G LEU* 3.8 18.4 - - + -
172G VAL 3.4 23.6 - - - +
173G TYR* 3.5 32.8 - - + +
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Residues in contact with THR 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F GLY 5.6 1.6 - - - +
102G LYS* 5.5 4.5 + - - +
103G VAL* 1.3 73.1 - - - +
105G VAL* 1.3 63.5 + - - +
106G GLU* 3.7 19.9 + - + +
144G SER* 3.6 16.8 + - - +
146G VAL* 3.9 27.8 - - + -
170G VAL 3.2 3.1 - - - +
171G LEU* 3.6 0.7 - - - -
172G VAL* 2.7 47.3 + - - +
174G LEU* 4.1 23.1 + - + +
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 4.6 5.8 - - + -
104G THR* 1.3 73.0 - - - +
106G GLU* 1.3 61.5 + - - +
126G ALA* 3.4 40.7 - - + +
129G VAL* 3.8 31.9 - - + -
130G LYS 4.9 0.4 - - - +
133G LEU* 5.0 0.7 - - + -
143G ILE* 3.9 25.6 - - + -
144G SER 2.9 9.2 - - - -
145G ILE* 3.5 3.9 - - + -
146G VAL 3.0 24.0 + - - +
169G ALA* 4.0 13.7 - - + -
170G VAL 3.3 7.9 - - - +
171G LEU* 4.6 8.1 - - + -
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Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F GLY 5.8 0.3 - - - +
104G THR* 4.0 20.3 - - + +
105G VAL* 1.3 73.9 - - - +
107G GLY* 1.3 57.6 + - - +
108G HIS* 3.4 20.9 + - - +
126G ALA* 4.7 0.2 - - - -
146G VAL* 3.1 9.6 - - + +
148G TYR* 3.9 28.8 + - + -
152G LYS* 5.9 1.9 - - - +
169G ALA* 3.2 2.1 - - - -
170G VAL* 2.6 44.8 + - + +
172G VAL* 3.7 30.0 - - + +
174G LEU* 5.2 5.9 - - - +
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Residues in contact with GLY 107 (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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105G VAL 3.6 3.2 + - - -
106G GLU* 1.3 71.8 - - - +
108G HIS* 1.3 67.5 + - - -
122G GLY* 3.4 26.0 - - - -
125G ARG* 5.1 0.2 - - - -
126G ALA* 4.1 6.2 - - - +
146G VAL 3.0 10.0 + - - -
147G SER* 3.5 1.8 + - - -
148G TYR 3.0 25.6 + - - -
168G ARG 3.7 4.9 - - - -
169G ALA* 4.2 4.3 - - - -
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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