Contacts of the strand formed by residues 244 - 249 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91P ASN* 3.5 29.9 + - - +
186P THR* 3.8 1.4 + - - +
187P ARG* 3.5 2.6 - - - -
188P ASN* 2.8 45.9 + - - +
189P ASN* 4.7 11.6 + - - +
242P GLY 4.8 0.9 - - - +
243P ASP* 1.3 73.4 - - - +
245P PHE* 1.3 63.7 + - - +
246P GLU* 2.8 38.0 + - - +
256P ALA* 3.9 10.2 - - - +
257P ALA 3.5 4.5 - - - +
258P THR* 3.5 24.5 + - + +
179S LYS* 3.7 12.1 - - - +
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Residues in contact with PHE 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ILE* 3.1 45.5 - - + -
137P LEU* 4.7 13.5 - - + -
185P MET* 4.2 14.4 - - + -
186P THR 3.4 12.1 - - - -
187P ARG* 3.6 32.3 - - + -
192P VAL* 4.4 2.2 - - + -
237P VAL* 3.6 9.9 - - + -
238P ALA 3.9 13.2 - - - -
239P VAL* 4.0 11.4 - - + -
243P ASP* 3.5 24.0 - - + -
244P ARG* 1.3 78.0 - - - +
246P GLU* 1.3 61.4 + - - +
256P ALA* 3.1 5.2 - - - +
257P ALA* 2.8 38.8 + - + +
259P PHE* 4.0 14.1 - + + -
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Residues in contact with GLU 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P LEU* 5.3 0.2 - - - -
184P LYS 4.0 0.9 - - - +
185P MET* 3.3 3.7 - - - -
186P THR* 2.9 44.8 + - - +
244P ARG* 2.8 33.7 + - - +
245P PHE* 1.3 75.9 - - - +
247P ALA* 1.3 63.4 + - - +
248P HIS* 3.6 31.9 + - + +
254P SER* 3.8 13.9 + - - -
255P VAL 3.2 9.3 - - - +
256P ALA* 4.3 3.0 - - + +
179S LYS* 3.4 18.3 + - - -
180S ASN* 5.1 2.3 - - - +
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Residues in contact with ALA 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P ALA* 3.8 20.6 - - + -
137P LEU* 3.8 24.8 - - + +
183P MET* 4.8 2.2 - - + -
184P LYS 3.3 8.3 - - - +
185P MET* 4.2 7.0 - - + -
246P GLU* 1.3 73.1 - - - +
248P HIS* 1.3 63.6 + - - +
249P ILE* 5.2 2.2 - - + -
254P SER* 3.1 8.8 - - - -
255P VAL* 2.8 38.0 + - + +
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Residues in contact with HIS 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P ALA 3.5 1.6 - - - +
183P MET* 3.2 6.9 - - - +
184P LYS* 2.9 42.5 + - + +
186P THR* 5.9 5.4 - - + -
246P GLU* 3.6 34.8 - - + +
247P ALA* 1.3 79.9 - - - +
249P ILE* 1.3 62.3 + - - +
250P GLU 4.0 0.4 - - - -
253P GLY 3.6 4.7 + - - +
254P SER* 3.9 12.2 - - - -
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Residues in contact with ILE 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P ALA* 4.7 5.8 - - + -
107P GLU 3.6 27.1 - - - +
108P ILE* 4.5 3.8 - - + -
135P PRO* 3.7 23.1 - - + -
136P ALA 4.5 2.2 - - - +
181P CYS* 3.9 19.7 - - + +
182P ALA 3.5 2.0 - - - -
183P MET* 4.1 7.9 - - + -
233P LEU* 3.8 25.1 - - + -
247P ALA* 5.2 1.3 - - + -
248P HIS* 1.3 78.6 - - - +
250P GLU* 1.3 64.2 + - - +
251P GLY 3.3 0.7 + - - -
252P ILE* 3.0 32.1 + - + -
253P GLY* 2.8 38.3 + - - +
255P VAL* 5.0 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