Contacts of the strand formed by residues 37 - 44 (chain H) in PDB entry 1CVJ
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 ILE 37 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASP* 2.5 24.4 + - - +
47F ILE* 4.7 11.8 - - + +
28H TYR* 3.9 19.5 - - + -
31H PHE* 3.9 12.1 - - + -
32H SER* 3.9 23.8 - - - +
35H GLY 3.7 13.0 - - - +
36H PRO* 1.3 74.1 - - - +
38H LEU* 1.3 65.4 + - - +
39H SER* 3.4 19.1 - - - +
40H ILE* 3.5 27.4 - - + -
57H VAL* 4.3 1.8 - - + -
58H ASN 3.1 14.6 - - - +
59H PHE* 4.0 12.3 - - + +
60H GLN* 3.2 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 5.8 2.2 + - - +
47F ILE* 4.4 15.1 - - - +
37H ILE* 1.3 75.0 - - - +
39H SER* 1.3 66.7 + - - +
58H ASN* 2.7 24.0 + - + +
59H PHE* 3.7 19.1 - - - +
60H GLN* 3.9 19.5 - - + +
998H A 5.2 10.3 - - + +
993O A 3.7 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 6.0 2.7 - - - +
37H ILE* 3.4 1.7 - - - +
38H LEU* 1.3 84.4 - - - +
40H ILE* 1.3 69.9 + - - +
41H ARG* 6.2 0.4 - - - -
58H ASN* 2.5 63.5 + - - +
998H A 3.6 16.8 + - - -
6T A 4.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE 5.1 1.8 + - - +
49F ARG* 3.7 19.3 + - + +
24H GLU* 3.5 27.2 - - + +
27H LEU* 3.9 35.9 - - + -
28H TYR* 4.7 17.0 - - + +
31H PHE* 5.2 1.3 - - + -
37H ILE* 3.5 26.5 - - + -
39H SER* 1.3 94.2 - - - +
41H ARG* 1.3 65.2 + - - +
56H TYR 3.3 7.0 - - - +
57H VAL* 3.2 36.3 - - + -
58H ASN* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLU* 4.0 4.0 - - - -
39H SER* 6.2 0.2 - - - -
40H ILE* 1.3 76.7 - - - +
42H VAL* 1.3 65.9 + - - +
43H CYS* 4.0 14.4 + - - -
55H ALA* 2.9 5.8 - - - +
56H TYR* 2.8 33.8 + - - +
998H A 4.7 9.3 + - - -
6T A 2.8 72.3 + - + -
7T A 2.9 80.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 4.5 5.2 - - + -
22H VAL 4.3 13.2 - - - +
23H THR* 4.2 3.8 - - - -
24H GLU* 3.4 29.8 + - + +
27H LEU* 3.4 33.7 - - + -
41H ARG* 1.3 73.4 - - - +
43H CYS* 1.3 63.2 + - - +
44H ARG* 3.4 21.0 + - + +
51H SER* 3.7 24.0 - - - +
54H TYR 4.2 4.3 - - - +
55H ALA* 3.4 8.7 - - + -
7T A 3.0 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ARG* 4.2 7.9 - - - +
42H VAL* 1.3 71.3 - - - +
44H ARG* 1.3 53.2 + - - +
51H SER* 3.6 5.0 + - - -
52H LEU* 2.7 36.9 + - + +
54H TYR* 3.3 57.6 + - + +
55H ALA* 4.9 0.2 - - - -
56H TYR* 3.9 22.2 - - - -
5T A 4.1 6.3 - - - +
6T A 4.2 14.6 - - - -
7T A 4.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F THR* 6.0 3.4 - - - -
24F GLU* 3.5 30.5 + - - +
25F ALA* 5.6 1.8 - - - +
44F ARG* 3.0 23.0 - - - +
23H THR* 6.0 1.2 - - - +
24H GLU* 3.0 22.6 + - - +
42H VAL* 3.4 23.9 + - + +
43H CYS* 1.3 79.0 - - - +
45H ASP* 1.3 67.4 + - - +
46H MET 3.4 1.6 + - - -
49H ARG* 3.1 42.8 - - - +
50H ARG 3.2 4.3 - - - -
51H SER* 3.9 9.9 - - - +
52H LEU* 3.8 5.8 - - - +
7R A 4.2 1.2 + - - -
5T A 4.0 8.1 - - - -
7T A 2.8 54.7 + - - +
----------------------------------------------------------
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