Contacts of the strand formed by residues 244 - 249 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179R LYS* 3.7 12.5 - - - +
91S ASN* 3.4 30.5 + - - +
186S THR* 3.8 1.0 + - - +
187S ARG* 3.5 2.1 - - - -
188S ASN* 2.8 46.3 + - - +
189S ASN* 4.7 11.1 + - - +
242S GLY 3.5 1.3 + - - +
243S ASP* 1.3 73.2 - - - +
245S PHE* 1.3 64.2 + - - +
246S GLU* 2.8 38.8 + - - +
256S ALA* 3.9 10.6 - - - +
257S ALA 3.5 4.0 - - - +
258S THR* 3.6 25.1 + - + +
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Residues in contact with PHE 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S ILE* 3.1 45.1 - - + -
137S LEU* 4.4 13.6 - - + +
185S MET* 4.3 13.7 - - + -
186S THR 3.3 12.8 - - - -
187S ARG* 3.5 31.2 - - + -
192S VAL* 4.4 1.8 - - + -
237S VAL* 3.5 12.1 - - + -
238S ALA 3.8 13.5 - - - -
239S VAL* 4.0 10.1 - - + -
243S ASP* 3.5 24.5 - - + -
244S ARG* 1.3 77.8 - - - +
246S GLU* 1.3 60.2 + - - +
256S ALA* 3.2 5.6 - - - +
257S ALA* 2.8 38.3 + - + +
259S PHE* 3.9 16.4 - + + -
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Residues in contact with GLU 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R LYS* 3.4 18.0 + - - -
180R ASN* 5.2 1.7 - - - +
137S LEU* 5.3 0.4 - - - -
184S LYS 4.0 0.9 - - - +
185S MET* 3.3 4.2 - - - +
186S THR* 2.8 47.7 + - - +
244S ARG* 2.8 34.1 + - - +
245S PHE* 1.3 76.6 - - - +
247S ALA* 1.3 64.1 + - - +
248S HIS* 3.6 30.0 + - + +
254S SER* 3.9 13.5 + - - -
255S VAL 3.2 8.8 - - - +
256S ALA* 4.4 2.6 - - + +
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Residues in contact with ALA 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S ALA* 3.8 29.2 - - + -
137S LEU* 3.8 16.9 - - + +
183S MET* 4.8 2.0 - - + -
184S LYS 3.3 7.9 - - - +
185S MET* 4.0 7.2 - - + +
246S GLU* 1.3 75.8 - - - +
248S HIS* 1.3 63.6 + - - +
249S ILE* 4.2 2.0 - - + -
254S SER* 3.2 8.8 - - - -
255S VAL* 2.9 37.0 + - + +
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Residues in contact with HIS 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182S ALA 3.5 1.4 - - - +
183S MET* 3.2 6.4 - - - +
184S LYS* 2.8 44.6 + - + +
186S THR* 5.9 4.9 - - + -
246S GLU* 3.6 34.0 - - + +
247S ALA* 1.3 81.1 - - - +
249S ILE* 1.3 63.5 - - - +
250S GLU 4.0 0.4 - - - -
253S GLY 3.7 4.5 + - - +
254S SER* 3.9 12.7 - - - -
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Residues in contact with ILE 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S ALA* 4.7 5.4 - - + -
107S GLU 3.6 27.1 - - - +
108S ILE* 4.6 3.1 - - + -
135S PRO* 3.8 22.4 - - + -
136S ALA 4.6 2.0 - - - +
181S CYS* 3.9 19.7 - - + +
182S ALA 3.4 4.3 - - - +
183S MET* 4.0 8.5 - - + -
233S LEU* 3.8 23.3 - - + -
247S ALA* 5.3 1.1 - - + -
248S HIS* 1.3 78.5 - - - +
250S GLU* 1.3 65.4 + - - +
251S GLY 3.3 0.5 + - - -
252S ILE* 3.0 31.4 + - + -
253S GLY* 2.8 36.4 + - - +
255S VAL* 5.0 4.3 - - + -
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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