Contacts of the strand formed by residues 130 - 135 (chain A) in PDB entry 2G98
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 TRP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS* 3.3 25.3 - - + +
88A ARG 3.7 8.2 - - - +
89A ILE* 3.7 36.2 - - + +
104A PHE 3.7 13.5 - - - -
105A THR 4.2 2.2 - - - -
106A GLU 3.4 26.7 - - - -
125A VAL* 3.9 11.4 - - + -
127A GLU 3.0 18.0 + - - -
128A GLY 3.6 10.8 - - - -
129A SER* 1.3 77.2 - - - +
131A VAL* 1.3 64.2 + - - +
132A LEU 3.9 0.4 - - - -
144A LEU* 3.5 6.2 - - - +
145A LEU* 2.9 47.0 + - + +
166A LEU* 3.9 24.9 - - + -
167A ARG 3.1 23.6 - - - -
168A ARG* 3.7 17.9 - - + -
169A VAL* 4.1 2.0 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 4.0 18.2 - - + -
56A PHE* 3.8 28.3 - - + -
130A TRP* 1.3 75.3 - - - +
132A LEU* 1.3 65.2 + - - +
133A TYR* 3.5 35.4 - - + +
142A GLN* 4.1 8.1 - - + +
143A TYR 3.6 9.2 - - - +
144A LEU* 4.4 7.9 - - + -
166A LEU* 3.6 1.1 - - - -
167A ARG* 2.7 38.7 + - + +
169A VAL* 3.7 22.7 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.6 5.2 - - + -
123A LEU* 3.9 18.6 - - + -
130A TRP 3.9 1.4 - - - -
131A VAL* 1.3 71.6 - - - +
133A TYR* 1.3 59.6 + - - +
142A GLN* 3.5 4.2 - - - -
143A TYR* 2.9 43.3 + - + +
145A LEU* 4.1 16.7 - - + +
156A TRP* 3.4 44.0 - - + +
163A VAL* 3.5 32.3 - - + -
165A SER 3.9 1.8 - - - -
166A LEU* 2.6 35.0 - - + -
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.2 7.1 - - - +
131A VAL* 3.5 38.1 - - + +
132A LEU* 1.3 74.7 - - - +
134A GLU* 1.3 54.8 + - - +
135A LEU 3.2 0.3 + - - -
138A TYR* 3.3 52.5 - + + -
139A ARG* 3.5 13.5 - - - +
141A ARG 3.4 3.8 - - - -
142A GLN* 3.5 36.4 + - + -
143A TYR* 5.1 0.9 - - - -
162A ARG 4.8 0.4 - - - -
163A VAL* 3.5 5.1 - - - -
164A GLY 2.8 29.3 + - - -
165A SER* 3.1 27.6 + - - +
167A ARG* 3.1 34.5 + - + -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR* 1.3 73.8 - - - +
135A LEU* 1.3 78.3 - - + +
139A ARG 3.7 0.2 + - - -
140A GLY* 3.4 6.0 - - - -
141A ARG* 2.8 52.9 + - + +
143A TYR* 4.6 5.9 - - - +
160A ASN* 4.7 4.0 - - - +
162A ARG* 2.5 62.4 + - + +
163A VAL 3.5 8.1 + - - -
164A GLY* 3.2 11.0 + - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.2 0.5 - - - +
134A GLU* 1.3 106.7 - - + +
136A SER* 1.3 64.5 + - - +
138A TYR 3.7 0.3 + - - -
139A ARG* 3.1 25.9 + - + +
140A GLY* 3.8 22.9 - - - +
162A ARG* 4.6 9.0 - - - -
164A GLY* 3.7 6.7 - - - -
165A SER* 2.9 19.4 + - - -
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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