Contacts of the strand formed by residues 252 - 257 (chain A) in PDB entry 3NIG
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 GLU 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 3.4 6.2 - - - +
242A GLY 3.1 34.2 + - - +
243A GLU* 3.3 15.2 - - - +
244A PHE* 2.8 36.8 + - + +
245A ASP* 3.1 17.0 - - - +
250A THR* 3.1 26.1 + - - -
251A THR* 1.3 77.7 - - - +
253A TYR* 1.3 65.3 + - - +
254A VAL* 5.3 0.4 - - - -
269A ILE* 4.2 11.2 - - + -
270A LEU 3.3 8.1 - - - +
271A ASP* 4.5 4.2 - - - +
277A LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 4.2 17.6 - - + +
180A GLU* 4.9 3.6 + - - -
182A VAL* 4.0 22.9 - - + +
195A LEU* 4.1 15.3 - - + -
197A GLN* 3.6 24.4 + - + +
239A VAL* 5.4 1.1 - - + -
240A ALA 3.7 5.2 - - - +
241A VAL* 4.0 10.8 - - + -
251A THR* 4.2 14.1 - - + -
252A GLU* 1.3 81.7 - - - +
254A VAL* 1.3 62.8 + - - +
255A VAL* 4.2 1.3 - - + -
268A GLU 3.6 0.9 - - - +
269A ILE* 3.2 6.1 - - - +
270A LEU* 2.8 50.4 + - + +
271A ASP 4.1 9.2 - - - -
272A SER* 3.8 27.8 + - - -
274A TYR* 3.9 35.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 3.3 8.7 - - - +
240A ALA* 2.8 44.8 + - + +
241A VAL* 4.8 2.7 - - - -
242A GLY 5.0 0.2 - - - +
244A PHE* 3.8 20.9 - - + -
253A TYR* 1.3 76.4 - - - +
255A VAL* 1.3 63.0 + - - +
267A VAL* 3.8 16.4 - - + -
268A GLU 3.4 3.8 - - - +
269A ILE* 4.3 10.3 - - + -
293A VAL* 4.1 13.6 - - + +
295A VAL* 3.8 22.7 - - + -
306A LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.5 25.1 - - + -
235A TRP* 3.8 28.1 + - + +
236A GLY* 3.4 35.7 - - - +
238A SER 3.7 2.9 - - - +
239A VAL* 4.5 1.1 - - + -
253A TYR* 4.6 0.2 - - + -
254A VAL* 1.3 83.1 - - - +
256A GLY* 1.3 61.8 + - - +
257A ALA* 3.9 1.7 + - - +
267A VAL* 3.3 7.7 - - - -
268A GLU* 2.9 35.7 + - - +
270A LEU* 3.5 29.4 - - + -
293A VAL* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR 3.4 0.2 - - - +
236A GLY 2.8 30.2 + - - -
237A TYR 3.3 9.7 + - - -
238A SER* 2.9 28.4 + - - -
254A VAL 4.3 0.4 - - - -
255A VAL* 1.3 71.9 - - - +
257A ALA* 1.3 56.0 + - - -
258A PRO* 3.7 5.6 - - - -
266A ALA 3.9 4.9 - - - -
267A VAL* 4.4 4.3 - - - -
290A GLY* 3.5 11.4 - - - -
293A VAL* 4.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY 3.3 13.9 - - - +
234A TYR 3.7 1.3 - - - -
235A TRP* 3.7 31.0 - - + -
255A VAL 5.0 0.7 - - - +
256A GLY* 1.3 72.5 - - - -
258A PRO* 1.3 66.9 - - - +
259A THR 3.2 4.1 + - - -
260A TRP* 3.2 19.3 + - + -
266A ALA* 2.9 35.9 + - + +
268A GLU* 6.3 0.7 - - + -
290A GLY 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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