Contacts of the strand formed by residues 92 - 101 (chain A) in PDB entry 2IIJ
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 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.3 3.3 - - - +
88A ASP* 2.9 14.4 - - - +
91A GLY* 1.3 72.9 - - - -
93A THR* 1.3 64.0 + - - +
112A TYR* 4.3 17.3 - - + -
113A VAL 3.8 3.1 - - - -
114A ASN* 3.1 26.2 - - - +
140A LEU* 5.9 0.7 - - + -
122B LYS* 2.9 44.7 + - + +
123B ASP* 4.2 12.6 - - - +
126B LEU* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.7 14.3 + - + -
45A VAL* 3.0 35.9 - - + +
88A ASP* 2.6 28.3 + - - +
92A VAL* 1.3 73.3 - - - +
94A VAL* 1.3 65.8 + - - +
112A TYR* 3.2 8.0 - - - -
113A VAL* 2.7 42.4 + - + -
115A ASN* 2.8 20.0 + - - -
126B LEU* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE 3.6 0.3 - - - +
44A TYR* 3.7 0.3 - - - -
45A VAL* 2.8 31.9 + - + +
93A THR* 1.3 85.4 - - - +
95A VAL* 1.3 66.8 + - - +
96A LEU* 4.0 9.0 - - + +
110A GLY* 3.6 17.0 - - - -
111A TYR 3.4 2.9 - - - -
112A TYR* 3.3 35.4 - - + +
113A VAL* 3.9 3.1 - - - +
126B LEU* 3.3 30.2 - - + +
130B ILE* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.8 25.8 - - + -
24A PHE* 4.0 19.6 - - + -
42A ILE* 3.1 33.0 - - + -
43A ILE 3.1 2.2 - - - +
44A TYR* 3.6 28.3 - - + -
94A VAL* 1.3 76.3 - - - +
96A LEU* 1.3 59.7 + - - +
97A ILE 4.0 0.3 + - - -
109A VAL* 2.9 12.1 - - - +
111A TYR* 2.7 31.0 + - + +
113A VAL* 4.2 8.7 - - + -
139A ILE* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS 3.3 2.1 - - - +
43A ILE* 2.7 65.5 + - + +
45A VAL* 5.2 1.6 - - + -
94A VAL* 4.2 5.6 - - + -
95A VAL* 1.3 70.9 - - - +
97A ILE* 1.3 63.0 + - - +
98A THR* 3.5 21.5 - - + -
108A ARG* 3.5 30.1 - - + -
109A VAL 2.7 11.4 - - - +
110A GLY* 3.8 6.5 - - - -
129B ARG* 3.7 27.1 - - + +
130B ILE* 3.8 16.8 - - + -
134B ARG* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.3 46.4 - - + -
26A ILE* 3.7 14.4 - - + -
40A TRP* 4.0 21.7 - - + -
41A LYS 2.9 14.1 - - - +
42A ILE* 3.9 17.3 - - + -
74A PHE* 3.7 24.2 - - + -
96A LEU* 1.3 72.0 - - - +
98A THR* 1.3 59.3 + - - +
99A CYS 3.5 1.7 + - - -
107A ILE* 3.4 6.4 - - - +
108A ARG* 3.3 3.6 + - - -
109A VAL* 3.0 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU 3.2 0.3 - - - +
41A LYS* 3.0 22.6 + - - +
43A ILE* 3.4 14.2 - - - +
96A LEU* 3.5 17.3 - - + -
97A ILE* 1.3 72.6 - - - +
99A CYS* 1.3 59.6 + - - +
100A THR* 3.1 10.7 + - - -
105A GLU* 2.9 42.9 + - - +
107A ILE 2.8 8.3 - - - -
108A ARG* 3.2 34.1 - - + +
134B ARG* 3.7 2.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.1 35.7 - - - -
39A GLU 3.4 1.8 - - - -
40A TRP* 3.2 44.0 - - + +
97A ILE 3.5 1.0 + - - -
98A THR* 1.3 70.7 - - - +
100A THR* 1.3 57.4 + - - +
105A GLU* 3.2 1.0 - - - -
106A PHE* 2.7 49.2 + - + -
107A ILE* 3.1 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 4.4 0.9 - - - +
39A GLU* 2.7 63.0 + - - +
41A LYS* 5.0 2.8 - - - +
98A THR* 3.1 18.0 + - - -
99A CYS* 1.3 73.4 - - - +
101A TYR* 1.3 58.9 + - - +
102A ARG 3.9 1.6 + - - -
103A GLY* 3.5 35.1 + - - +
104A GLN 3.3 3.4 - - - +
105A GLU* 3.3 25.8 + - + +
106A PHE* 3.8 0.4 - - - -
134B ARG* 5.7 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.2 32.2 - - + +
35A SER* 3.0 18.7 + - - -
36A GLU* 2.7 38.2 + - + +
37A ASP 3.5 13.7 - - - -
38A LEU* 3.8 11.9 - - + -
100A THR* 1.3 71.6 - - - +
102A ARG* 1.3 91.9 + - + +
103A GLY 3.2 0.4 - - - -
104A GLN* 2.8 25.3 + - - +
106A PHE* 3.5 21.8 - - + -
151A ILE* 3.3 13.9 - - + +
153A TRP* 3.1 54.6 + + + +
----------------------------------------------------------
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