Contacts of the strand formed by residues 276 - 285 (chain C) in PDB entry 2IGT
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 VAL 276 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 4.4 0.4 - - - -
9C ALA* 3.4 24.5 - - + +
11C HIS* 3.7 41.7 - - + +
274C GLY 3.9 1.0 + - - -
275C GLY* 1.3 74.6 - - - +
277C VAL* 1.3 72.2 + - - +
278C ALA* 4.7 2.2 - - + +
305C ARG 3.5 1.6 - - - +
306C TRP* 3.4 4.3 - - - +
307C GLU* 3.0 41.6 + - + +
309C LYS* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 3.8 24.2 - - + -
9C ALA 2.9 12.3 + - - +
10C GLU* 3.2 4.7 - - - -
11C HIS 2.9 22.3 + - - -
263C HIS* 3.4 20.2 - - + +
266C MSE 3.7 24.7 - - + +
267C ARG* 4.1 10.8 - - + -
276C VAL* 1.3 78.3 - - - +
278C ALA* 1.3 61.0 + - - +
279C SER* 3.6 7.0 - - - +
304C SER* 3.4 26.0 - - - +
305C ARG 3.3 4.3 - - - +
306C TRP* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C HIS* 3.2 26.7 - - + +
14C VAL* 4.3 9.9 - - + -
276C VAL* 4.1 3.0 - - + -
277C VAL* 1.3 72.1 - - - +
279C SER* 1.3 61.3 + - - +
303C PHE* 3.4 10.8 - - + -
304C SER* 3.4 0.9 - - - -
305C ARG* 2.8 58.7 + - - +
307C GLU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C HIS 3.2 7.3 + - - +
12C VAL* 3.8 5.6 - - - +
13C PRO* 3.5 6.4 - - - +
14C VAL* 2.7 29.1 + - - +
259C PHE 4.3 4.5 - - - -
263C HIS* 2.7 44.3 + - - +
277C VAL* 3.6 0.5 - - - +
278C ALA* 1.3 71.7 - - - +
280C GLY* 1.3 53.4 + - - +
303C PHE* 3.3 22.2 - - - -
304C SER* 2.8 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 4.8 0.2 - - - -
14C VAL 3.2 11.0 - - - -
15C ILE* 5.0 0.9 - - - -
259C PHE* 3.3 33.9 - - - +
279C SER* 1.3 79.1 - - - +
281C GLU* 1.3 58.1 + - - -
302C LEU* 3.4 2.1 - - - -
303C PHE* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL 3.4 3.4 + - - -
15C ILE* 3.5 20.5 - - + +
16C LEU 2.9 25.1 + - - +
258C SER* 6.0 0.9 - - - -
259C PHE* 3.9 24.0 + - + -
280C GLY* 1.3 77.9 - - - +
282C LEU* 1.3 60.3 + - - +
283C VAL* 4.0 5.9 - - + +
299C SER* 2.6 37.0 + - - +
301C SER 3.4 5.2 - - - +
302C LEU* 4.1 18.8 - - + +
303C PHE* 3.6 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.4 28.9 - - + +
115C GLU* 3.4 45.1 - - + +
116C GLN* 3.5 31.9 - - - +
118C VAL* 3.8 16.6 - - + -
119C HIS* 4.0 16.4 - - + +
281C GLU* 1.3 70.3 - - - +
283C VAL* 1.3 67.5 + - - +
299C SER* 4.0 0.2 + - - -
300C THR* 2.9 31.5 + - - -
301C SER* 3.0 19.0 + - - +
303C PHE* 4.2 5.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.0 24.7 - - + -
16C LEU 2.8 15.9 + - - +
17C GLU* 3.8 24.5 - - + +
18C SER* 2.9 34.5 + - - -
281C GLU* 4.2 7.0 - - + +
282C LEU* 1.3 82.3 - - - +
284C ILE* 1.3 60.6 + - - +
297C VAL* 3.5 28.9 - - + -
298C LEU 3.5 6.5 - - - +
299C SER* 3.7 21.8 - - - +
300C THR* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 5.1 0.2 - - - -
18C SER* 4.6 10.3 - - - +
24C PHE* 4.0 30.7 - - + -
26C LEU* 3.8 25.1 - - + +
36C GLU* 6.1 0.2 - - - +
115C GLU* 3.6 36.6 - - + +
283C VAL* 1.3 76.6 - - - +
285C ARG* 1.3 72.5 + - - +
297C VAL* 3.5 3.1 - - - +
298C LEU* 2.8 45.5 + - + +
300C THR* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 2.7 48.4 + - + +
18C SER 4.3 9.0 + - - +
26C LEU* 4.3 2.6 + - - +
284C ILE* 1.3 85.3 - - - +
286C GLU* 1.3 74.0 + - - +
287C ALA* 3.4 7.1 + - - +
294C PRO* 4.0 21.3 - - - +
295C GLY 3.0 34.2 + - - +
296C ARG* 3.4 6.5 - - - +
297C VAL* 3.4 28.7 - - + +
----------------------------------------------------------
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