Contacts of the strand formed by residues 183 - 187 (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 MET 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ALA* 3.8 30.5 - - + +
181D CYS 4.6 1.3 - - - +
182D ALA* 1.3 75.8 - - - +
184D LYS* 1.3 79.8 + - - +
185D MET* 3.8 11.4 - - + -
193D SER* 4.1 7.2 - - - +
194D SER* 3.0 40.6 - - - -
195D GLY 2.8 22.9 + - - +
233D LEU* 3.8 17.3 - - + -
234D GLY* 3.4 37.9 - - - +
247D ALA* 4.8 0.7 - - + -
248D HIS 3.2 10.1 - - - +
249D ILE* 3.9 9.9 - - + -
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Residues in contact with LYS 184 (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* 5.6 4.5 - - + -
183D MET* 1.3 82.4 - - - +
185D MET* 1.3 61.2 + - - +
186D THR* 4.3 5.2 - - + -
191D GLU* 3.5 31.8 + - + +
193D SER 3.7 5.2 - - - -
194D SER* 4.7 4.0 - - - -
246D GLU 4.0 0.5 - - - +
247D ALA* 3.3 1.7 - - - +
248D HIS* 2.8 42.0 + - + +
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Residues in contact with MET 185 (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* 3.9 28.7 - - + +
105D GLU* 4.4 6.7 - - - -
106D ALA* 4.5 9.0 - - + +
137D LEU* 3.9 25.1 - - - -
183D MET* 3.8 10.1 - - + -
184D LYS* 1.3 76.2 - - - +
186D THR* 1.3 71.5 + - - +
191D GLU* 3.5 3.3 - - - -
192D VAL* 2.9 29.9 + - + +
193D SER* 2.9 36.2 + - - +
235D PRO 4.7 0.7 - - - +
237D VAL* 3.9 12.1 - - + -
245D PHE* 4.3 12.1 - - + -
246D GLU 3.3 13.2 - - - +
247D ALA* 4.0 6.3 - - + -
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Residues in contact with THR 186 (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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184D LYS* 5.5 4.5 - - + -
185D MET* 1.3 78.8 - - - +
187D ARG* 1.3 59.2 + - - +
189D ASN* 3.9 14.9 + - - +
190D GLU* 3.3 29.6 - - - +
191D GLU* 4.0 7.9 - - + +
192D VAL* 4.0 3.4 - - - -
244D ARG 3.8 0.9 + - - +
245D PHE* 3.4 8.8 - - - -
246D GLU* 2.8 45.1 + - - +
248D HIS* 5.9 5.6 - - + -
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Residues in contact with ARG 187 (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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186D THR* 1.3 71.4 - - - +
188D ASN* 1.3 85.8 + - - +
189D ASN 3.0 1.6 + - - -
190D GLU* 3.0 26.2 + - - +
192D VAL* 3.7 28.6 - - + +
237D VAL* 4.0 10.2 - - - +
238D ALA* 3.0 27.3 + - - +
240D ASN* 4.2 11.1 + - - -
243D ASP* 3.2 30.3 + - + -
244D ARG 3.5 3.6 - - - +
245D PHE* 3.5 23.6 - - + -
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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