Contacts of the strand formed by residues 136 - 142 (chain B) in PDB entry 2G73
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 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 4.2 17.9 - - + +
50B ARG 3.5 7.6 - - - +
51B ARG* 5.6 0.4 - - - -
52B ALA* 3.9 0.4 - - - +
65B SER 5.6 0.4 - - - +
87B GLU* 4.1 17.9 - - - +
88B LEU* 4.0 19.1 - - + -
131B ILE* 3.6 35.8 - - + +
132B ASN 2.8 16.0 + - - +
133B ASP* 3.6 16.4 - - - +
135B GLU* 1.3 83.4 - - + +
137B MET* 1.3 58.6 + - - +
138B ASP 3.4 27.1 - - - +
139B TYR* 4.8 0.2 - - + -
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 4.8 4.3 - - + +
109A PRO* 3.4 34.8 - - + +
110A SER* 5.6 1.6 - - - +
50B ARG* 3.0 44.2 + - + +
51B ARG 3.0 23.8 - - - +
52B ALA* 4.0 11.2 - - + +
53B LEU* 3.8 33.9 - - + +
60B GLY* 3.8 16.8 - - - -
131B ILE* 5.9 0.7 - - - -
133B ASP* 5.2 2.9 - - - +
136B VAL* 1.3 72.0 - - - +
138B ASP* 1.3 68.3 + - + +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 4.1 20.1 - - + +
50B ARG* 2.8 37.4 + - + -
62B TRP* 3.5 20.8 - - - -
131B ILE* 6.2 0.4 - - - -
136B VAL* 3.4 8.3 - - - +
137B MET* 1.3 87.4 - - + +
139B TYR* 1.3 91.0 + - - +
140B GLN* 5.2 1.6 + - - -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.5 21.3 - - + -
48B VAL 3.2 15.0 - - - +
49B THR* 4.1 7.4 - - + -
62B TRP* 3.8 7.1 - - - -
129B LEU* 3.5 24.8 - - + +
131B ILE* 3.7 33.4 - - + +
138B ASP* 1.3 93.0 + - - +
140B GLN* 1.3 80.9 + - - +
141B TRP* 4.1 14.4 - + - -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 3.5 44.9 - - + +
46B LEU 3.6 1.0 - - - +
47B LEU* 3.6 5.0 - - - +
48B VAL* 2.7 39.8 + - + +
62B TRP* 4.5 6.1 - - + -
138B ASP* 5.2 1.8 + - - -
139B TYR* 1.3 89.0 + - - +
141B TRP* 1.3 68.3 + - - +
142B CYS* 3.7 13.0 - - - -
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Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 4.3 0.4 - - - -
40B PHE 4.1 1.8 - - - -
41B ASN* 3.4 51.4 - - + -
45B GLN* 3.7 29.3 + - - +
46B LEU 3.5 2.2 - - - -
47B LEU* 3.3 48.0 - - + -
125B THR* 3.8 19.7 - - + -
129B LEU* 3.9 38.1 - - + +
139B TYR* 4.1 12.2 - + - -
140B GLN* 1.3 80.8 - - - +
142B CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 3.1 45.3 - - - +
45B GLN* 3.3 6.1 - - - +
46B LEU* 2.6 40.9 + - - +
48B VAL* 4.5 3.6 - - + -
140B GLN* 3.7 19.3 - - - -
141B TRP* 1.3 79.5 - - - +
143B ASP* 1.3 67.0 + - - +
146B ASP* 5.4 3.1 - - + -
147B VAL* 3.7 21.1 - - + -
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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