Contacts of the strand formed by residues 240 - 244 (chain A) in PDB entry 2W3S
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 GLY 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A THR* 3.1 22.3 + - - +
238A PRO 3.3 1.4 + - - -
239A ASP* 1.3 80.3 - - - +
241A TYR* 1.3 69.5 + - - -
341A LEU 3.4 8.3 - - - -
343A LYS* 2.7 42.1 + - - -
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Residues in contact with TYR 241 (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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235A ARG 3.8 3.4 - - - +
236A GLU* 3.8 37.0 + - + -
237A THR* 3.9 2.0 - - - +
240A GLY* 1.3 78.0 - - - -
242A GLY* 1.3 61.1 + - - +
243A ILE* 3.6 6.5 + - + +
255A PHE* 3.3 43.1 - + + -
259A PRO* 3.7 33.2 - - + +
260A HIS* 4.7 4.5 - + - -
340A THR* 3.2 4.8 - - - -
341A LEU* 2.7 45.0 + - + +
342A PRO 3.9 14.6 - - - -
343A LYS* 3.7 27.9 + - + +
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Residues in contact with GLY 242 (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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233A GLN 3.4 5.4 - - - +
234A ILE* 3.6 0.9 - - - -
235A ARG* 2.8 43.4 + - - +
237A THR* 4.5 7.8 - - - +
241A TYR* 1.3 70.0 - - - +
243A ILE* 1.3 61.9 + - - -
338A SER* 5.3 3.4 - - - -
339A VAL 3.6 6.3 - - - -
340A THR* 4.2 10.3 - - - +
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Residues in contact with ILE 243 (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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233A GLN 3.9 1.6 - - - -
234A ILE* 3.8 23.6 - - + -
241A TYR* 4.0 7.2 - - + +
242A GLY* 1.3 75.0 - - - -
244A GLY* 1.3 63.7 + - - +
247A VAL* 3.9 8.1 - - + -
252A LEU* 3.7 18.4 - - + -
255A PHE* 3.6 37.2 - - + -
281A ILE* 3.3 26.5 - - + +
338A SER* 3.1 2.9 - - - -
339A VAL* 2.7 48.1 + - + +
341A LEU* 3.9 26.9 - - + -
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Residues in contact with GLY 244 (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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230A ASP 5.9 0.2 - - - -
231A LEU 3.4 11.7 - - - -
233A GLN 3.0 22.6 + - - -
242A GLY 3.9 0.4 + - - -
243A ILE* 1.3 73.1 - - - +
245A ALA* 1.3 64.3 + - - -
246A GLY 3.2 3.6 - - - -
247A VAL* 3.1 14.8 + - - +
281A ILE* 3.3 13.3 - - - +
337A GLU 3.9 1.8 - - - -
338A SER* 3.7 10.8 - - - -
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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