Contacts of the strand formed by residues 244 - 249 (chain K) in PDB entry 2WQT
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 ARG 244 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91K ASN* 3.5 25.7 + - - +
186K THR 3.6 1.0 - - - +
187K ARG* 3.4 3.5 - - - -
188K ASN* 2.9 47.8 + - - +
189K ASN* 4.9 8.2 + - - +
242K GLY 4.9 1.1 - - - +
243K ASP* 1.3 72.1 - - - +
245K PHE* 1.3 63.7 + - - +
246K GLU* 3.0 32.7 + - - +
256K ALA* 3.7 12.6 - - - +
257K ALA 3.5 4.3 - - - +
258K THR* 3.9 23.4 + - + +
179N LYS* 3.5 20.0 - - - +
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Residues in contact with PHE 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K ILE* 3.0 45.5 - - + -
137K LEU* 4.2 13.9 - - + +
185K MET* 4.2 13.0 - - + -
186K THR 3.3 12.1 - - - -
187K ARG* 3.5 33.7 - - + -
192K VAL* 4.3 2.7 - - + -
237K VAL* 3.6 9.6 - - + -
238K ALA 3.8 12.3 - - - -
239K VAL* 3.8 11.2 - - + -
243K ASP* 3.6 20.9 - - + -
244K ARG* 1.3 76.7 - - - +
246K GLU* 1.3 60.4 + - - +
255K VAL 4.0 0.4 - - - +
256K ALA* 3.1 6.1 - - - +
257K ALA* 2.8 42.3 + - + +
259K PHE* 3.8 17.9 - + + -
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Residues in contact with GLU 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LYS 3.9 0.9 - - - +
185K MET* 3.3 4.4 - - - +
186K THR* 2.8 48.1 + - - +
244K ARG* 3.0 32.8 + - - +
245K PHE* 1.3 75.4 - - - +
247K ALA* 1.3 62.2 + - - +
248K HIS* 3.6 32.3 + - + +
254K SER* 4.0 10.6 + - - -
255K VAL 3.3 6.3 - - - +
256K ALA* 4.4 3.3 - - + +
179N LYS* 3.1 20.8 + - - -
180N ASN* 5.1 1.7 - - - +
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Residues in contact with ALA 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K ALA* 3.9 20.4 - - + -
137K LEU* 3.7 27.0 - - + +
183K MET* 4.9 0.4 - - - -
184K LYS 3.4 7.2 - - - +
185K MET* 4.1 6.7 - - + +
246K GLU* 1.3 76.0 - - - +
248K HIS* 1.3 64.5 + - - +
249K ILE* 5.3 1.8 - - + -
254K SER* 3.1 8.1 - - - -
255K VAL* 2.8 38.6 + - + +
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Residues in contact with HIS 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K ALA 3.6 1.1 - - - +
183K MET* 3.2 7.6 - - - +
184K LYS* 2.9 40.7 + - + +
246K GLU* 3.6 34.1 + - + +
247K ALA* 1.3 76.5 - - - +
249K ILE* 1.3 63.7 + - - +
250K GLU 4.0 0.9 - - - +
253K GLY 3.6 5.2 - - - +
254K SER* 3.6 20.0 + - - -
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Residues in contact with ILE 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K ALA* 4.6 3.8 - - + -
107K GLU 3.3 30.1 - - - +
108K ILE* 4.2 3.6 - - + -
135K PRO* 3.7 22.9 - - + -
136K ALA 4.2 4.0 - - - +
181K CYS* 4.1 14.6 - - + +
182K ALA 3.5 4.0 - - - +
183K MET* 3.9 7.9 - - + -
233K LEU* 3.7 28.0 - - + -
247K ALA* 5.3 1.1 - - + -
248K HIS* 1.3 78.2 - - - +
250K GLU* 1.3 67.7 + - - +
251K GLY 3.4 0.3 + - - -
252K ILE* 3.0 41.1 + - + -
253K GLY 2.8 21.6 + - - +
255K VAL* 4.9 3.6 - - + -
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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