Contacts of the strand formed by residues 73 - 79 (chain A) in PDB entry 2COC
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 HIS 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 4.5 0.6 - - - -
72A GLY* 1.3 81.8 + - - +
74A VAL* 1.3 61.2 + - - +
87A SER* 3.5 1.8 - - - -
88A ALA* 2.8 32.7 + - - +
89A SER 3.9 7.6 + - - -
90A SER* 3.4 30.5 - - - -
91A ALA* 3.2 32.1 + - + +
94A GLN* 3.6 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.9 12.8 - - + -
62A VAL* 4.3 6.2 - - - +
63A PRO* 3.0 21.5 - - + +
69A LEU* 3.6 28.9 - - + -
71A SER 4.2 14.6 - - - +
72A GLY 3.7 4.3 + - - +
73A HIS* 1.3 76.1 - - - +
75A TRP* 1.3 74.9 + - - +
85A TYR* 3.7 18.8 - - + -
86A LEU 3.3 24.2 - - - +
87A SER* 3.5 11.7 - - - +
94A GLN* 4.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.1 13.7 - - + -
38A LEU* 5.9 0.7 - - + -
60A LEU* 3.5 23.6 - - + +
61A SER 4.4 1.8 - - - +
62A VAL* 4.3 11.9 - - + +
63A PRO* 3.6 6.7 - - - -
74A VAL* 1.3 81.0 - - - +
76A LYS* 1.3 60.3 + - - +
77A LEU* 3.6 20.5 - - + +
84A TRP 4.2 0.2 - - - +
85A TYR* 3.6 0.9 - - - -
86A LEU* 3.0 72.1 + - + +
88A ALA* 3.7 22.0 - - + -
94A GLN* 3.6 26.0 - - + +
97A TRP* 3.2 43.7 - + + -
98A LEU* 3.9 20.6 - - + -
101A LEU* 4.0 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 5.0 7.3 + - - +
59A LYS 4.6 0.2 - - - -
60A LEU* 3.9 1.0 - - - -
61A SER* 2.7 51.0 + - - +
63A PRO* 3.6 6.6 - - + +
75A TRP* 1.3 76.0 - - - +
77A LEU* 1.3 71.1 + - - +
78A GLN* 3.5 31.6 - - + -
83A SER* 3.9 21.2 + - - -
84A TRP 3.7 6.1 - - - +
85A TYR* 3.6 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.7 4.5 - - + -
53A ILE* 5.5 12.1 - - + -
58A CYS* 3.9 26.0 - - + -
59A LYS 3.6 15.5 - - - +
60A LEU* 3.8 23.1 - - + -
75A TRP* 3.6 24.5 - - + +
76A LYS* 1.3 80.8 - - - +
78A GLN* 1.3 58.2 + - - +
79A TRP* 4.0 17.9 - - + -
82A GLN 3.9 0.2 - - - +
83A SER* 3.4 4.7 - - - -
84A TRP 3.0 33.8 + - - +
86A LEU* 3.7 19.3 - - + -
101A LEU* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 4.9 0.3 - - - +
59A LYS* 3.5 40.3 + - + +
61A SER* 6.3 0.4 - - - -
76A LYS* 3.5 23.9 - - + -
77A LEU* 1.3 73.6 - - - +
79A TRP* 1.3 63.7 + - - +
81A LYS* 5.8 1.5 - - - +
82A GLN 3.1 18.8 - - - +
83A SER* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO* 4.2 9.2 - - + -
52A THR 4.9 1.6 - - - -
53A ILE* 3.2 43.7 - - + -
54A PRO* 3.1 27.8 - - + +
57A SER* 3.2 23.3 - - - +
58A CYS* 3.1 24.2 - - - -
77A LEU* 4.0 26.0 - - + -
78A GLN* 1.3 75.0 - - - +
80A ALA* 1.3 75.3 + - + +
81A LYS 3.0 3.8 - - - +
82A GLN* 2.6 49.1 + - + +
84A TRP* 3.5 37.0 - + + -
----------------------------------------------------------
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