Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 1J7H
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 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 6.5 0.9 - - + -
58A VAL* 5.8 3.1 - - + -
62A ILE* 4.6 15.0 - - + -
68A THR 3.7 2.6 + - - +
69A ALA* 2.8 48.3 + - + +
70A ALA 4.1 3.6 - - - +
71A ASP* 1.3 75.5 - - - +
73A VAL* 1.3 57.8 + - - +
74A LYS 3.1 7.9 - - - +
75A THR* 3.0 29.8 - - + +
95A PHE* 6.0 0.4 - - + -
96A PHE* 4.1 12.8 - - + -
103A ASN* 4.1 6.4 + - - -
105A PRO* 3.0 31.0 - - + +
125A ALA* 3.8 9.2 - - + -
126A ILE 3.0 20.4 - - - +
127A ALA* 3.8 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.5 2.5 - - + -
71A ASP 3.0 0.9 + - - +
72A ILE* 1.3 73.4 - - - +
74A LYS* 1.3 73.0 + - + +
103A ASN* 5.2 0.7 - - - +
105A PRO* 3.1 5.7 - - - +
106A ALA 2.8 17.7 + - - -
126A ILE* 2.8 37.5 + - + +
128A VAL* 3.0 49.6 - - + +
4B GLN* 3.2 40.3 - - + +
22B VAL* 3.3 13.7 - - - +
24B LEU* 4.3 0.7 - - + -
29B LEU* 5.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.1 2.9 - - - +
73A VAL* 1.3 89.1 - - + +
75A THR* 1.3 78.2 + - - +
76A THR* 3.8 13.3 + - - +
105A PRO* 3.8 0.4 - - - -
106A ALA* 3.2 31.9 - - + +
107A ARG 4.8 1.8 - - - -
108A SER* 4.3 19.2 - - - -
125A ALA* 3.0 2.0 - - - +
126A ILE* 2.7 40.6 + - + +
22B VAL* 5.1 3.1 - - + -
29B LEU* 5.0 22.0 - - + +
30B THR 5.0 11.0 - - - +
31B SER* 5.5 0.4 - - - +
124B GLU* 5.6 5.6 - - - -
126B ILE* 5.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.0 20.5 - - + +
74A LYS* 1.3 79.7 + - - +
76A THR* 1.3 69.4 + - - +
77A VAL* 4.0 18.6 - - + -
92A TYR* 3.1 31.0 + - + +
105A PRO* 3.7 4.4 - - - +
106A ALA 2.6 19.9 + - - +
107A ARG* 3.2 7.3 - - - +
108A SER* 2.9 23.0 + - - -
123A ILE* 4.8 6.1 - - + -
124A GLU 3.7 0.2 - - - -
125A ALA* 3.2 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 3.8 13.5 + - - -
75A THR* 1.3 74.4 - - - +
77A VAL* 1.3 67.6 + - - +
78A PHE* 3.5 26.0 - - + -
108A SER* 2.7 43.7 - - - +
109A CYS* 4.8 0.2 - - - -
123A ILE* 4.2 0.3 - - - +
124A GLU* 2.8 54.0 + - + +
78B PHE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 4.0 10.8 - - + -
76A THR* 1.3 85.1 - - - +
78A PHE* 1.3 71.7 + - - +
79A VAL* 3.8 9.2 + - + +
85A PHE* 5.2 2.9 - - + -
88A VAL* 5.9 6.7 - - + -
92A TYR* 5.2 4.3 - - + -
107A ARG* 3.5 22.9 - - - +
108A SER 3.5 3.0 + - - -
109A CYS* 2.9 42.4 - - + +
110A VAL 3.3 1.6 + - - -
121A LEU* 4.9 6.5 - - + -
122A GLU 2.7 22.9 - - - +
123A ILE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.5 22.7 - - + -
77A VAL* 1.3 74.2 - - - +
79A VAL* 1.3 62.1 + - - +
108A SER 4.6 0.9 - - - -
110A VAL* 3.5 16.6 - - + -
112A VAL* 3.6 23.3 - - + -
115A LEU* 3.5 15.7 - - + -
121A LEU* 3.1 10.4 - - - +
122A GLU* 3.0 36.9 + - + -
124A GLU* 2.8 37.7 - - + -
78B PHE* 6.2 2.7 - + - -
76C THR* 6.2 0.4 - - + -
78C PHE* 6.2 2.7 - + - -
108C SER* 4.1 11.9 - - - -
110C VAL* 3.2 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.4 10.3 - - + +
78A PHE* 1.3 79.4 - - - +
80A LYS* 1.3 60.5 + - - +
81A ASP 4.0 9.9 - - - +
82A LEU* 3.8 25.4 - - + +
85A PHE* 3.6 32.1 - - + -
88A VAL* 5.8 5.8 - - + -
109A CYS* 5.5 0.4 - - + -
110A VAL* 2.9 18.0 + - - +
111A GLU* 3.1 21.4 - - + +
112A VAL* 3.1 26.6 + - - +
115A LEU* 4.7 0.4 - - - -
120A GLY 4.2 3.4 - - - +
121A LEU* 5.2 4.9 - - + -
----------------------------------------------------------
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