Contacts of the strand formed by residues 244 - 249 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C LYS* 3.8 11.7 - - - +
91D ASN* 3.4 30.3 + - - +
186D THR* 3.8 1.2 + - - +
187D ARG* 3.5 1.7 - - - -
188D ASN* 2.8 46.4 + - - +
189D ASN* 4.7 10.5 + - - +
242D GLY 3.6 1.1 + - - +
243D ASP* 1.3 74.1 - - - +
245D PHE* 1.3 62.8 + - - +
246D GLU* 2.8 37.7 + - - +
256D ALA* 3.9 10.4 - - - +
257D ALA 3.5 4.7 - - - +
258D THR* 3.5 26.9 + - + +
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Residues in contact with PHE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 3.1 45.1 - - + -
137D LEU* 4.7 13.7 - - + -
185D MET* 4.3 12.8 - - + -
186D THR 3.4 13.9 - - - -
187D ARG* 3.5 31.0 - - + -
192D VAL* 4.4 1.6 - - + -
237D VAL* 3.5 12.8 - - + -
238D ALA 3.8 13.2 - - - -
239D VAL* 4.0 10.1 - - + -
243D ASP* 3.5 24.2 - - + -
244D ARG* 1.3 77.4 - - - +
246D GLU* 1.3 62.3 + - - +
255D VAL 4.6 0.2 - - - -
256D ALA* 3.1 5.4 - - - +
257D ALA* 2.7 39.3 + - + +
259D PHE* 3.9 15.9 - + + -
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C LYS* 3.4 18.1 + - - -
180C ASN* 5.2 1.6 - - - +
137D LEU* 5.3 0.4 - - - -
184D LYS 4.0 0.5 - - - +
185D MET* 3.3 4.3 - - - -
186D THR* 2.8 48.1 + - - +
244D ARG* 2.8 34.8 + - - +
245D PHE* 1.3 75.5 - - - +
247D ALA* 1.3 61.9 + - - +
248D HIS* 3.6 31.5 + - + +
254D SER* 3.9 13.2 + - - -
255D VAL 3.2 10.3 - - - +
256D ALA* 4.2 2.3 - - + +
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Residues in contact with ALA 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ALA* 3.8 28.3 - - + -
137D LEU* 3.8 16.7 - - + +
183D MET* 4.8 2.2 - - + -
184D LYS 3.3 8.7 - - - +
185D MET* 4.0 8.1 - - + +
246D GLU* 1.3 75.8 - - - +
248D HIS* 1.3 63.6 + - - +
249D ILE* 4.2 2.7 - - + -
254D SER* 3.1 8.3 - - - -
255D VAL* 2.8 37.4 + - + +
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ALA 3.5 1.9 - - - +
183D MET* 3.2 7.1 - - - +
184D LYS* 2.8 44.8 + - + +
186D THR* 5.9 6.1 - - + -
246D GLU* 3.6 34.9 - - + +
247D ALA* 1.3 79.3 - - - +
249D ILE* 1.3 62.7 + - - +
250D GLU 4.0 0.7 - - - +
253D GLY 3.7 4.5 - - - +
254D SER* 3.9 12.4 - - - -
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Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ALA* 4.6 5.8 - - + -
107D GLU 3.6 27.4 - - - +
108D ILE* 4.5 3.6 - - + -
135D PRO* 3.8 21.3 - - + -
136D ALA 4.6 1.8 - - - +
181D CYS* 3.9 17.7 - - + +
182D ALA 3.4 4.7 - - - +
183D MET* 3.9 8.3 - - + -
233D LEU* 3.7 26.0 - - + -
247D ALA* 5.3 1.3 - - + +
248D HIS* 1.3 77.0 - - - +
250D GLU* 1.3 66.9 + - - +
251D GLY 3.3 0.5 + - - -
252D ILE* 3.0 44.0 + - + -
253D GLY* 2.8 23.4 + - - +
255D 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