Contacts of the strand formed by residues 122 - 127 (chain B) in PDB entry 2XWA
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 LEU 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLY 3.5 5.3 + - - +
121B THR* 1.3 78.8 - - - +
123B CYS* 1.3 61.8 + - - +
145B LEU* 4.3 29.9 - - + +
146B LEU 3.4 7.4 - - - +
147B PRO* 3.8 32.8 - - + -
188B VAL 4.6 0.9 - - - +
189B CYS* 4.7 3.6 - - - -
190B GLY 4.9 2.8 + - - -
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Residues in contact with CYS 123 (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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121B THR* 4.0 5.8 - - - -
122B LEU* 1.3 78.7 - - - +
124B ASP* 1.3 63.5 + - - +
125B VAL 3.9 0.5 + - - -
144B VAL 3.7 0.5 - - - +
145B LEU* 3.4 5.9 - - - -
146B LEU* 2.9 34.6 + - - +
148B VAL* 3.6 25.4 - - + -
187B LEU* 3.5 21.7 - - + +
188B VAL 3.2 5.8 - - - +
189B CYS* 2.0 49.6 - - - -
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 2.7 37.5 + - - -
14B TYR* 4.3 5.6 + - - +
123B CYS* 1.3 71.9 - - - +
125B VAL* 1.3 63.5 + - - +
126B ALA* 4.6 0.5 - - - +
143B HIS* 2.9 30.8 + - - +
144B VAL 3.6 6.0 - - - +
145B LEU* 3.9 16.2 - - + +
186B PRO 3.4 3.1 - - - +
187B LEU* 4.5 0.7 - - - -
188B VAL* 2.7 46.4 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ILE* 3.9 19.2 - - + +
123B CYS 4.8 0.2 - - - +
124B ASP* 1.3 76.3 - - - +
126B ALA* 1.3 66.5 + - - +
143B HIS* 3.3 2.0 - - - -
144B VAL* 3.0 40.7 + - + +
146B LEU* 3.5 32.3 - - + -
178B SER* 4.3 5.6 - - - -
182B ASP* 5.7 0.4 - - + -
186B PRO 3.4 14.8 - - - +
187B LEU* 4.1 13.0 - - + -
197B VAL* 4.0 23.1 - - + -
213B TYR* 4.1 7.4 - - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ILE* 4.2 5.8 - - - +
12B ARG* 4.0 26.7 - - - +
14B TYR* 5.8 0.4 - - - +
15B MET* 3.4 23.8 - - - +
124B ASP* 4.3 0.9 - - - +
125B VAL* 1.3 80.2 - - - +
127B GLY* 1.3 59.0 + - - +
141B LEU* 3.9 11.7 - - + -
142B GLN 3.2 15.3 - - - +
143B HIS* 4.0 4.0 - - + -
182B ASP* 4.5 2.1 - - - +
185B GLY* 4.4 4.2 - - - -
186B PRO* 3.7 14.7 + - + +
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Residues in contact with GLY 127 (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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1B ILE* 3.7 4.7 - - - +
15B MET* 3.9 7.9 - - - -
27B GLY* 5.8 1.1 - - - -
126B ALA* 1.3 75.8 - - - +
128B TRP* 1.3 58.7 + - - -
129B GLY 3.3 0.7 + - - -
141B LEU* 3.4 14.7 - - - +
142B GLN* 3.0 36.8 + - - +
181B GLY 5.4 0.2 - - - -
182B ASP* 3.1 20.3 - - - +
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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