Contacts of the strand formed by residues 142 - 149 (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 GLN 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ILE* 3.8 18.5 - - + +
4B GLY 4.7 1.6 - - - -
5B ARG* 3.4 24.3 + - - +
6B GLU* 3.6 13.3 + - - +
7B ALA* 4.5 0.9 - - - -
126B ALA* 3.2 9.0 - - - +
127B GLY 3.0 32.6 + - - +
131B VAL* 3.9 17.2 - - + +
136B ARG* 5.7 1.9 - - - +
138B PRO* 3.7 30.4 - - + +
140B SER* 3.0 27.1 + - - -
141B LEU* 1.3 82.8 + - - +
143B HIS* 1.3 61.8 + - - +
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Residues in contact with HIS 143 (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* 4.0 3.8 - - - -
4B GLY* 3.4 1.9 - - - -
5B ARG* 3.0 65.3 + - + +
6B GLU 4.1 1.3 + - - -
7B ALA* 3.8 21.7 - - + -
12B ARG* 3.2 24.2 + - - -
124B ASP* 2.9 23.7 + - - +
125B VAL 3.3 12.3 - - - +
126B ALA* 4.0 9.6 - - + -
142B GLN* 1.3 75.8 - - - +
144B VAL* 1.3 67.8 + - - +
145B LEU* 5.1 9.0 - - + -
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Residues in contact with VAL 144 (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* 3.8 21.1 - - + -
2B LEU 4.8 0.9 - - - +
3B GLY 3.5 24.7 - - - +
4B GLY* 4.1 1.3 - - - -
123B CYS 3.7 0.3 - - - +
124B ASP* 3.6 5.4 - - - +
125B VAL* 3.0 49.7 + - + +
143B HIS* 1.3 80.3 - - - +
145B LEU* 1.3 66.6 + - - +
146B LEU* 3.9 14.8 - - + -
176B ARG* 3.7 26.7 - - + -
177B ASP 4.6 7.0 - - - +
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Residues in contact with LEU 145 (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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122B LEU* 4.3 36.8 - - + +
123B CYS 3.4 22.4 - - - +
124B ASP* 3.9 18.8 - - + +
143B HIS* 4.8 9.2 + - + -
144B VAL* 1.3 80.8 - - - +
146B LEU* 1.3 66.6 + - - +
147B PRO* 4.4 3.4 - - - +
176B ARG* 4.5 8.3 + - - -
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Residues in contact with LEU 146 (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 3.4 0.5 - - - +
122B LEU* 3.9 4.0 - - - -
123B CYS* 2.9 34.3 + - - +
125B VAL* 3.5 27.4 - - + -
144B VAL* 3.9 11.9 - - + -
145B LEU* 1.3 82.8 - - - +
147B PRO* 1.3 72.0 - - + +
148B VAL* 3.6 0.7 + - - +
171B ALA* 4.1 13.9 - - + +
172B GLU 3.5 18.2 - - - +
176B ARG* 3.4 40.2 - - + +
177B ASP* 4.6 10.3 - - - +
187B LEU* 5.1 1.8 - - + -
213B TYR* 3.6 16.4 - - + +
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Residues in contact with PRO 147 (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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120B GLY* 4.4 11.7 - - - +
121B THR 3.3 7.4 - - - +
122B LEU* 4.0 17.9 - - + -
145B LEU 4.4 2.9 - - - +
146B LEU* 1.3 86.3 - - + +
148B VAL* 1.3 62.5 + - - +
171B ALA* 3.4 2.7 - - - -
172B GLU* 2.8 69.9 + - + +
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Residues in contact with VAL 148 (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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117B VAL* 3.9 15.0 - - + +
118B ALA 4.0 2.9 - - - +
119B PRO* 3.6 5.4 - - + +
120B GLY* 2.8 30.9 + - - +
121B THR* 2.8 22.1 + - - +
123B CYS* 3.6 25.1 - - + -
146B LEU 3.6 0.4 + - - +
147B PRO* 1.3 73.0 - - - +
149B LEU* 1.3 61.9 + - - +
150B ASP 4.1 0.2 + - - -
169B MET* 3.7 17.3 - - + -
170B CYS 3.4 6.7 - - - +
171B ALA* 4.2 3.6 - - + +
172B GLU* 5.3 1.4 - - - +
187B LEU* 5.3 1.8 - - + -
1230B GOL 3.4 39.9 - - - +
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Residues in contact with LEU 149 (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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147B PRO 3.5 1.0 + - - -
148B VAL* 1.3 75.0 - - - +
150B ASP* 1.3 86.0 + - - +
153B THR* 4.0 18.2 - - + -
154B CYS* 3.8 23.1 - - + +
159B HIS* 4.8 5.8 - - + +
170B CYS* 2.9 20.4 + - + +
172B GLU* 4.1 28.3 - - + +
210B PRO* 3.5 34.8 - - + -
1230B GOL 2.9 20.5 + - - -
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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