Contacts of the strand formed by residues 252 - 261 (chain A) in PDB entry 2WLJ
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE 3.5 6.9 + - - -
136A THR* 3.5 39.5 - - - +
138A PRO* 3.5 28.6 - - + +
246A HIS* 3.5 11.2 - - - -
247A HIS* 2.9 29.7 + - - +
250A PHE* 3.0 29.5 + - + +
251A ALA* 1.3 81.4 - - - +
253A ASN* 1.3 66.9 + - - +
254A VAL* 3.6 0.7 + - - +
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Residues in contact with ASN 253 (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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138A PRO* 5.2 2.8 - - - +
244A THR* 6.5 0.2 - - - -
245A GLY 3.4 6.7 - - - +
246A HIS* 2.9 33.4 + - - +
252A GLN* 1.3 81.7 - - - +
254A VAL* 1.3 65.0 + - - +
255A HIS* 3.3 25.1 + - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 4.0 32.1 - - + +
139A THR 4.2 2.0 - - - +
140A ALA* 3.7 31.0 - - + +
171A ILE* 4.3 11.4 - - + -
243A PHE* 4.6 2.0 - - + -
244A THR* 3.3 3.9 - - - -
245A GLY 2.9 42.1 + - - +
247A HIS* 3.9 33.2 - - + -
252A GLN 4.1 0.7 - - - +
253A ASN* 1.3 79.0 - - - +
255A HIS* 1.3 71.7 + - - +
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Residues in contact with HIS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO 6.1 0.4 - - - -
140A ALA* 3.5 13.1 + - - +
242A LEU* 4.7 2.7 - - + -
243A PHE* 3.2 11.2 - - - +
244A THR* 4.2 8.0 - - + +
253A ASN* 3.3 29.6 + - + +
254A VAL* 1.3 86.1 + - - +
256A ALA* 1.3 63.7 + - - +
172B ILE* 3.2 32.8 - - + +
173B GLU* 5.2 2.4 + - - -
246B HIS* 3.6 41.1 - + + -
248B GLU* 5.8 3.4 - - - +
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Residues in contact with ALA 256 (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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140A ALA* 4.0 15.7 - - + -
142A VAL* 4.2 12.3 - - + +
144A PHE* 3.9 23.0 - - + -
241A VAL 3.9 0.2 - - - +
242A LEU* 3.5 4.4 - - - +
243A PHE* 2.8 39.8 + - + +
255A HIS* 1.3 76.0 - - - +
257A ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 257 (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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18A ASP* 2.6 44.4 + - - +
19A GLY* 4.6 3.1 - - - -
20A SER* 3.4 19.6 - - - +
144A PHE* 3.6 9.6 - - - -
241A VAL 3.2 7.0 - - - +
242A LEU* 4.5 2.9 - - + -
256A ALA* 1.3 79.7 - - - +
258A HIS* 1.3 66.4 + - - +
170B GLN* 3.0 24.0 + - - -
172B ILE* 4.8 4.5 - - - -
207B ILE* 3.4 37.7 - - + -
248B GLU* 2.8 40.5 + - - +
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Residues in contact with HIS 258 (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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17A SER* 2.9 32.2 + - - -
18A ASP* 4.8 1.6 - - - -
19A GLY* 4.1 5.4 - - - +
144A PHE* 3.5 43.4 - - + +
145A SER 4.1 4.1 + - - -
146A SER* 5.0 5.4 + - - -
240A LEU* 3.6 3.5 - - - +
241A VAL* 2.9 34.4 + - + +
257A ARG* 1.3 78.2 + - - +
259A ALA* 1.3 83.5 + - - +
260A TYR* 3.4 38.4 - + - -
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Residues in contact with ALA 259 (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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13A ARG* 4.1 4.1 + - - -
15A LEU* 3.7 25.6 - - + +
16A ASN 3.4 20.2 - - - +
17A SER* 2.8 20.6 + - - -
19A GLY* 4.2 4.3 - - - -
238A GLU* 5.5 0.7 - - + +
239A PHE 3.1 10.5 - - - +
240A LEU* 4.2 5.8 - - + -
258A HIS* 1.3 90.1 + - - +
260A TYR* 1.3 65.2 + - - +
264A GLU* 4.1 2.1 - - - +
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Residues in contact with TYR 260 (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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13A ARG* 4.3 2.2 - - - -
144A PHE* 4.0 0.7 - - - +
145A SER* 2.7 35.6 + - - -
146A SER 3.6 20.6 - - - -
147A ARG* 3.8 7.6 - - - -
148A MET* 3.5 41.7 - - + -
161A MET* 3.5 26.7 - - + +
238A GLU* 3.3 7.0 - - - +
239A PHE* 2.7 46.0 + - + +
241A VAL* 3.9 21.8 - - + -
258A HIS* 3.4 24.5 - + - -
259A ALA* 1.3 79.9 - - - +
261A SER* 1.3 66.6 + - - +
264A GLU* 3.3 13.0 - - + +
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Residues in contact with SER 261 (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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13A ARG* 3.8 21.3 + - - +
236A HIS* 6.6 0.2 - - - -
237A SER 4.2 6.1 - - - -
238A GLU* 4.4 14.4 - - - -
239A PHE* 5.0 2.4 - - - -
260A TYR* 1.3 78.6 - - - +
262A CYS* 1.3 63.8 + - - +
263A ASP* 3.4 19.4 + - - -
264A GLU* 3.0 41.3 + - - +
265A ILE* 4.0 4.0 + - - +
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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