Contacts of the strand formed by residues 57 - 63 (chain C) in PDB entry 2GJD
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 57 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY 4.5 7.9 - - - +
25C TYR* 3.8 31.9 + - + +
44C GLY* 4.0 2.7 - - - -
45C ILE 3.5 18.2 - - - +
46C PRO* 4.3 12.8 - - + -
55C GLY 4.8 2.5 - - - +
56C GLY* 1.3 78.2 - - - +
58C TYR* 1.3 64.2 + - - +
59C PRO* 3.6 5.4 - - - +
155C TYR* 2.8 27.0 + - - +
157C LYS* 4.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLY* 3.4 1.7 - - - -
45C ILE* 2.8 54.0 + - + +
47C GLY* 3.8 14.6 - - - -
53C TRP* 2.8 56.5 + + - -
56C GLY* 3.7 7.7 - - - -
57C VAL* 1.3 72.0 - - - +
59C PRO* 1.3 69.3 - - + +
60C ILE* 4.3 0.3 - - - +
77C PHE* 3.7 21.1 - - + -
81C PHE* 3.7 22.7 - + + -
120C LEU* 3.8 15.0 - - + -
151C GLN* 3.9 16.2 - - + -
152C ALA* 3.3 20.1 + - - +
155C TYR* 3.7 24.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 4.2 11.7 - - - +
43C ALA 3.4 9.6 - - - +
44C GLY* 4.4 1.8 - - - -
57C VAL 3.6 3.6 - - - +
58C TYR* 1.3 84.5 - - + +
60C ILE* 1.3 65.7 - - - +
77C PHE* 3.5 3.1 - - - -
78C PRO* 3.4 32.5 - - + +
81C PHE* 5.2 0.2 - - + -
155C TYR* 3.4 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 3.5 5.4 - - - +
43C ALA* 2.9 51.8 + - + +
45C ILE* 4.0 25.1 - - + -
58C TYR 4.3 2.2 - - - +
59C PRO* 1.3 73.3 - - - +
61C THR* 1.3 63.2 + - - +
62C VAL* 3.9 14.6 - - + -
75C VAL* 3.7 22.7 - - + -
76C LYS 3.1 11.2 - - - +
77C PHE* 3.4 38.6 - - + -
92C ILE* 4.1 11.0 - - + -
112C ILE* 5.7 1.3 - - + -
113C VAL* 4.5 7.6 - - + -
116C VAL* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LYS* 5.0 15.0 - - - -
41C TRP 3.3 7.9 - - - +
42C GLU* 4.3 19.1 - - + +
60C ILE* 1.3 77.3 - - - +
62C VAL* 1.3 65.2 + - - +
63C GLU* 4.1 12.9 + - - -
74C LYS 3.6 1.3 - - - +
75C VAL* 3.4 5.0 - - - +
76C LYS* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN 3.8 0.5 - - - +
40C LYS* 3.4 4.2 - - - -
41C TRP* 2.9 40.8 + - + +
43C ALA* 4.7 7.9 - - + -
60C ILE* 3.9 25.1 - - + -
61C THR* 1.3 78.8 - - - +
63C GLU* 1.3 62.8 + - - +
64C TYR* 3.5 36.5 - - + +
73C PRO* 3.8 19.3 - - + -
74C LYS 3.5 2.2 - - - -
75C VAL* 4.4 11.4 - - + -
109C LEU* 4.4 18.6 - - + -
112C ILE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN 3.5 5.4 - - - +
40C LYS* 4.2 27.1 - - + +
61C THR* 4.6 8.6 + - - +
62C VAL* 1.3 77.8 - - - +
64C TYR* 1.3 63.3 + - - +
65C PRO* 3.6 2.3 - - - +
73C PRO* 3.3 2.8 - - - +
74C LYS* 2.8 57.9 + - + +
76C LYS* 4.2 23.6 + - - +
40D LYS* 5.4 5.7 + - - -
----------------------------------------------------------
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