Contacts of the strand formed by residues 2 - 12 (chain A) in PDB entry 1R6W
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 ARG 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A HIS 3.6 8.6 + - - +
1A MET* 1.3 89.1 - - - +
3A SER* 1.3 61.6 + - - +
35A ARG 3.2 4.3 - - - +
36A GLU* 3.2 31.4 + - + -
70A TRP* 2.9 69.7 + - + +
71A LEU* 3.8 25.0 - - + +
72A ALA 5.5 0.2 - - - -
73A GLY* 3.3 18.5 - - - +
74A ASP* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.1 3.5 + - - -
2A ARG* 1.3 75.6 - - - +
4A ALA* 1.3 66.2 + - - +
35A ARG* 2.8 54.2 + - - +
70A TRP* 3.6 4.2 - - - -
71A LEU* 3.5 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 1.3 81.1 + - - +
5A GLN* 1.3 65.0 + - - +
33A CYS 3.1 12.3 - - - +
34A LEU* 4.0 12.6 - - + -
35A ARG* 5.3 2.5 - - - -
67A VAL* 3.5 30.3 - - + -
71A LEU* 3.9 13.2 - - + +
320A LEU* 4.0 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 1.3 75.7 + - - +
6A VAL* 1.3 81.5 + - - +
7A TYR* 3.2 43.0 - - + +
31A TYR 4.0 0.2 - - - +
32A VAL* 3.5 4.0 - - - +
33A CYS* 2.8 38.0 + - + +
318A ARG* 3.7 24.1 - - + +
319A LEU 3.5 0.3 + - - -
320A LEU* 2.8 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 1.3 87.8 + - - +
7A TYR* 1.3 66.6 + - - +
30A LEU* 4.6 4.0 - - + -
31A TYR 3.3 9.2 - - - +
32A VAL* 4.2 6.7 - - + -
60A GLN* 5.7 0.7 - - + -
63A LEU* 3.7 21.1 - - + -
64A LEU* 3.9 27.6 - - + -
67A VAL* 4.1 22.0 - - + -
318A ARG* 3.6 1.0 - - - -
319A LEU* 2.8 50.5 + - + +
320A LEU* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.2 38.1 - - + +
6A VAL* 1.3 75.0 - - - +
8A ARG* 1.3 58.5 + - - +
9A TRP* 4.0 1.5 - - + -
30A LEU* 3.1 12.4 - - - +
31A TYR* 2.9 44.4 + + + +
33A CYS* 4.4 4.1 - - + +
42A TRP* 3.6 35.4 - + - -
313A VAL* 3.4 30.3 - - + +
316A LEU* 3.9 30.3 - - + -
317A GLU 3.1 15.5 - - - +
318A ARG* 3.8 21.2 - - + -
319A LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL 4.3 0.4 + - - -
7A TYR* 1.3 73.7 - - - +
9A TRP* 1.3 63.0 + - - +
29A GLY 3.7 3.6 - - - -
30A LEU* 4.0 6.1 - - + -
56A TRP* 3.3 38.3 - - + +
60A GLN* 3.1 42.6 + - - +
316A LEU* 4.7 0.9 - - - +
317A GLU* 2.9 71.3 + - - +
319A LEU* 4.0 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.0 9.9 - - + -
8A ARG* 1.3 80.6 - - - +
10A GLN* 1.3 72.6 + - - +
11A ILE* 3.6 17.9 - - + -
27A ARG* 3.5 27.6 - - + -
28A ASP* 3.5 1.9 - - - -
29A GLY* 3.0 45.7 + - - +
30A LEU 3.3 18.5 - - - -
31A TYR* 3.4 34.4 - + - -
44A GLU* 3.4 15.9 - - - -
46A SER* 3.4 28.3 - - - -
56A TRP* 3.5 3.6 - - - -
267A SER* 3.8 9.2 - - - -
299A GLN* 3.3 32.8 - - - +
316A LEU* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 1.3 79.2 - - - +
11A ILE* 1.3 65.1 + - - +
12A PRO* 3.9 6.8 - - - +
26A THR* 3.6 18.2 + - - +
27A ARG 3.3 5.2 - - - -
28A ASP* 2.8 28.5 + - - +
56A TRP* 3.8 21.4 - - + -
299A GLN* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.6 15.3 - - + -
10A GLN* 1.3 71.9 - - - +
12A PRO* 1.3 79.9 - - + +
13A MET* 3.3 0.5 + - - +
26A THR* 3.5 2.9 - - - -
27A ARG* 2.8 43.5 + - + +
267A SER* 3.5 31.9 - - - -
295A MET* 4.2 20.0 - - + -
297A ALA* 3.7 31.9 - - + +
299A GLN* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 3.9 7.0 - - - +
11A ILE* 1.3 91.5 - - + +
13A MET* 1.3 59.9 + - - +
25A LYS 4.0 6.1 - - - +
26A THR* 4.6 3.3 - - - +
295A MET 3.9 0.2 - - - -
296A GLN* 3.0 54.5 + - + +
297A ALA* 5.8 3.4 - - + -
----------------------------------------------------------
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