Contacts of the strand formed by residues 236 - 243 (chain U) in PDB entry 2NX5
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 GLN 236 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125U PRO* 3.9 30.5 - - - +
216U GLN* 2.9 8.9 + - - +
217U PHE* 2.8 46.1 + - + +
232U LYS 4.5 1.6 + - - -
233U PRO* 4.1 1.2 - - - +
234U VAL* 2.8 39.3 + - + +
235U THR* 1.3 74.8 - - - +
237U ILE* 1.3 64.5 + - - +
238U VAL* 3.9 19.0 - - + +
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Residues in contact with ILE 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214U GLN* 3.4 46.7 - - + +
215U VAL 3.3 10.3 - - - +
216U GLN* 3.3 30.1 - - + +
236U GLN* 1.3 76.9 - - - +
238U VAL* 1.3 64.8 + - - +
239U SER* 3.9 5.0 + - - +
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Residues in contact with VAL 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125U PRO* 5.0 0.9 - - + -
126U PRO* 3.5 41.5 - - + +
127U GLU* 4.8 1.3 - - + -
128U VAL* 3.3 34.0 - - + +
215U VAL 3.0 27.6 + - - +
236U GLN* 3.9 24.7 - - + +
237U ILE* 1.3 73.5 - - - +
239U SER* 1.3 63.9 + - - +
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Residues in contact with SER 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132T LYS* 4.3 10.4 + - - -
128U VAL* 4.1 7.0 - - - +
212U ARG* 4.1 27.9 + - - -
213U CYS 3.3 13.7 - - - -
214U GLN* 4.3 9.0 - - - -
237U ILE* 3.9 6.0 + - - -
238U VAL* 1.3 79.6 - - - +
240U ALA* 1.3 63.7 + - - +
241U GLU* 5.5 1.2 + - - +
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Residues in contact with ALA 240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132T LYS* 3.4 26.9 - - + +
128U VAL* 3.7 25.4 - - + +
130U VAL* 3.2 23.1 - - + +
212U ARG* 3.4 3.2 - - - +
213U CYS 2.8 30.8 + - - +
239U SER* 1.3 76.1 - - - +
241U GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T SER* 4.1 3.8 + - - +
132T LYS* 3.7 33.3 - - + +
130U VAL* 4.3 4.5 - - - -
210U HIS* 2.8 32.2 + - - +
211U PHE 3.3 13.7 - - - +
212U ARG* 3.7 17.5 - - + +
239U SER* 5.5 0.8 + - - +
240U ALA* 1.3 76.7 - - - +
242U ALA* 1.3 61.3 + - - +
243U TRP* 3.4 27.0 + - - +
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Residues in contact with ALA 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T SER* 3.4 22.7 - - - +
130U VAL* 3.9 19.5 - - + +
132U GLU* 3.9 8.3 - - + +
146U LEU* 5.2 0.7 - - + -
204U TRP* 4.6 11.9 - - + -
210U HIS* 3.9 2.8 - - - -
211U PHE* 2.9 38.0 + - + +
241U GLU* 1.3 74.3 - - - +
243U TRP* 1.3 71.7 + - - +
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Residues in contact with TRP 243 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204U TRP* 3.4 9.5 - - - -
207U PRO* 4.8 11.9 - - + +
208U ARG 5.6 1.3 - - - -
209U ASN 3.7 8.3 - - - +
210U HIS* 3.3 52.7 - + + -
211U PHE* 4.8 0.2 - - - -
241U GLU* 3.4 27.5 + - - +
242U ALA* 1.3 81.7 - - - +
244U GLY* 1.3 63.4 + - - +
245U ARG* 2.8 30.9 + - - +
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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