Contacts of the strand formed by residues 262 - 270 (chain A) in PDB entry 5NJ8
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 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 5.3 6.9 + - - -
130A THR* 4.6 12.9 + - - +
131A THR* 3.9 17.7 + - - +
132A ASP* 4.9 10.1 + - - +
245A TYR* 3.7 3.5 - - - -
246A LEU* 2.7 50.1 + - + +
249A GLN* 6.4 1.8 - - + -
261A PRO* 1.3 81.8 - - + +
263A LEU* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.0 3.1 - - - -
131A THR* 3.7 35.0 + - + +
174A LEU 5.9 0.2 - - - +
176A TRP* 3.7 32.3 - - + -
209A PRO* 4.8 4.7 - - + -
216A MET* 4.4 8.3 - - + -
243A LEU* 3.6 29.8 - - + -
244A LYS 3.9 4.0 - - - -
245A TYR* 3.7 48.2 - - + +
246A LEU* 3.8 3.5 - - - +
261A PRO 5.9 0.2 - - - +
262A GLN* 1.3 81.6 - - - +
264A ALA* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.8 2.0 - - + -
129A VAL 3.0 21.3 - - - +
130A THR* 4.2 4.0 - - + +
131A THR* 4.7 2.4 - - - +
243A LEU* 3.3 9.1 - - - +
244A LYS 2.9 31.3 + - - +
246A LEU* 3.7 18.6 - - + -
263A LEU* 1.3 81.5 - - - +
265A LEU* 1.3 57.9 + - - +
266A PHE* 3.6 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU 3.6 2.1 - - - +
128A VAL* 3.3 4.3 - - - +
129A VAL* 2.9 39.5 + - + +
170A PHE* 4.5 15.5 - - + -
173A GLN* 5.2 6.3 - - + +
174A LEU* 4.6 17.5 - - + +
218A ARG* 3.8 31.4 - - + -
220A PHE* 4.1 28.5 - - + -
239A PHE* 5.6 1.1 - - + -
242A LYS 4.4 1.6 - - - +
243A LEU* 3.9 22.9 - - + +
264A ALA* 1.3 71.1 - - - +
266A PHE* 1.3 68.2 + - - +
267A ALA* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.7 28.0 - + - -
83A PHE* 6.0 1.3 - + - -
127A LEU 3.6 3.8 - - - -
128A VAL* 3.3 23.8 - - + -
136A PHE* 5.1 2.2 - + - -
241A GLY* 3.4 0.5 - - - -
242A LYS 2.9 35.1 + - - +
244A LYS* 3.5 36.1 - - + -
245A TYR 4.9 0.2 - - - -
246A LEU* 3.5 27.1 - - + -
264A ALA* 3.6 25.4 - - + -
265A LEU* 1.3 74.0 - - - +
267A ALA* 1.3 60.5 + - - +
167B LEU* 3.3 32.8 - - + -
170B GLU* 5.6 1.8 - - + -
171B ALA* 3.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.6 8.9 - - - +
127A LEU* 2.9 36.6 + - + +
220A PHE* 6.0 0.2 - - + -
239A PHE* 4.6 15.7 - - + -
240A GLN 3.9 3.1 - - - +
241A GLY* 3.6 19.7 - - - +
265A LEU* 4.2 20.2 - - + -
266A PHE* 1.3 76.4 - - - +
268A ILE* 1.3 65.5 + - - +
171B ALA* 3.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.6 44.9 - - + -
125A PHE 3.7 3.4 - - - +
126A VAL* 4.4 2.7 - - + -
238A ASN 3.6 0.5 - - - +
239A PHE* 3.4 6.0 - - - -
240A GLN* 2.9 39.3 + - - +
267A ALA* 1.3 78.3 - - - +
269A ALA* 1.3 66.2 + - - +
270A THR* 3.8 22.2 - - + -
168B ILE* 3.9 28.0 - - + -
171B ALA* 4.3 4.5 - - + +
172B ALA* 3.7 27.6 - - + +
340B ILE* 5.9 0.2 - - + -
342B ARG* 5.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 4.0 0.7 - - - +
124A GLY* 3.2 25.9 - - - -
125A PHE* 2.9 51.9 + - + +
127A LEU* 5.5 1.0 - - + +
237A MET* 4.0 12.6 - - + -
238A ASN 3.9 3.1 - - - -
239A PHE* 4.3 14.8 - - + -
268A ILE* 1.3 75.2 - - - +
270A THR* 1.3 62.2 + - - +
271A PRO* 3.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 4.1 7.0 - - - +
237A MET* 3.8 2.2 - - - -
238A ASN* 2.6 68.1 + - - +
240A GLN* 4.7 11.2 - - + -
268A ILE* 3.8 17.0 - - + +
269A ALA* 1.3 74.2 - - - +
271A PRO* 1.3 63.3 - - - +
272A LEU* 3.2 8.2 + - - +
342B ARG* 3.5 28.5 - - - +
----------------------------------------------------------
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