Contacts of the strand formed by residues 110 - 118 (chain V) in PDB entry 1IR1
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 110 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ILE* 5.8 0.2 - - + -
156D GLN* 3.6 29.4 - - + -
159D ARG* 5.5 8.7 - - + -
160D ASP* 5.5 3.6 - - - +
165D TYR* 5.9 1.3 - - + -
104V PHE* 4.8 2.9 - - - -
105V ASP* 3.0 23.7 + - + +
108V ARG* 3.5 60.1 - - + +
109V GLN* 1.3 84.3 - - - +
111V GLN* 1.3 65.6 + - - +
112V CYS* 3.3 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 3.6 11.5 + - - +
187A ARG* 2.9 35.5 + - - +
159D ARG* 5.1 2.8 - - - -
160D ASP* 5.3 1.9 + - - +
165D TYR* 3.2 65.5 - - + +
166D GLY 4.5 0.5 + - - -
43V GLU* 5.1 1.6 + - - -
100V ARG* 6.3 0.6 - - - -
102V ILE* 3.7 30.5 - - + +
103V GLY 3.2 10.8 - - - +
104V PHE* 3.8 20.9 - - + +
110V VAL* 1.3 74.2 - - - +
112V CYS* 1.3 59.7 + - - +
113V VAL 3.3 5.8 - - - +
114V SER* 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLY* 3.4 22.6 - - - +
396D ASP* 4.3 8.0 - - - +
32V TYR* 5.3 1.2 - - - -
38V TRP* 3.6 42.1 - - + -
103V GLY 3.0 5.8 + - - +
105V ASP* 3.6 20.9 - - - -
108V ARG* 4.0 12.6 - - - -
110V VAL* 3.3 25.3 + - - -
111V GLN* 1.3 72.3 - - - +
113V VAL* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 4.6 1.8 - - - -
166D GLY* 4.6 4.5 - - - -
432D ASN* 5.9 0.9 - - - +
29V GLN* 5.4 3.8 - - - +
32V TYR* 4.2 15.9 - - + -
33V LEU* 4.0 22.9 - - + -
38V TRP* 3.6 28.3 - - + -
101V ILE 4.2 3.4 - - - +
102V ILE* 3.2 4.3 - - - +
103V GLY* 3.0 29.9 + - - +
111V GLN* 3.3 4.9 - - - +
112V CYS* 1.3 86.2 - - - +
114V SER* 1.3 71.1 + - - +
115V PHE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 3.9 35.6 + - - +
166D GLY* 5.0 0.8 - - - -
13V GLU* 5.5 2.8 - - - +
14V THR* 3.7 22.5 + - - +
100V ARG* 4.2 12.3 + - - -
101V ILE 3.2 8.3 - - - -
102V ILE* 3.6 17.3 - - - +
111V GLN* 4.5 0.7 + - - -
113V VAL* 1.3 80.9 - - - +
115V PHE* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V TYR 5.3 2.7 - - - -
14V THR* 3.7 18.4 - - + +
15V LEU* 4.1 17.5 - - + -
21V LEU* 4.3 14.6 - - + -
26V LEU* 3.4 31.4 - - + -
29V GLN* 3.8 29.4 - - + -
30V VAL* 4.7 5.4 - - + -
33V LEU* 5.6 0.9 - - + -
100V ARG* 3.2 5.5 - - - +
101V ILE* 2.9 58.2 + - + +
113V VAL* 3.7 27.8 - - + -
114V SER* 1.3 77.0 + - - +
116V ILE* 1.3 75.5 + - - +
117V ALA* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V TYR* 3.9 44.1 + - + +
14V THR 5.0 1.2 + - - -
21V LEU* 5.2 4.5 - - - +
67V TRP* 4.3 20.2 - - + -
98V PHE* 5.1 3.4 - - + -
99V ILE 3.7 8.5 - - - +
100V ARG* 3.9 21.3 - - + +
115V PHE* 1.3 80.6 - - - +
117V ALA* 1.3 61.9 + - - +
118V TYR 3.7 10.8 - - - +
119V LYS* 3.5 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V LEU* 6.3 0.4 - - - -
26V LEU* 4.3 16.5 - - + +
87V LEU* 4.1 23.4 - - + +
91V LYS* 5.7 0.9 + - - +
99V ILE 2.8 10.2 + - - +
101V ILE* 3.8 34.1 - - + -
115V PHE* 3.5 5.5 + - + -
116V ILE* 1.3 73.9 - - - +
118V TYR* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87V LEU* 4.7 1.8 - - + -
91V LYS* 3.6 41.5 - - + -
94V TYR 4.2 4.3 - - - -
95V PRO* 2.8 38.3 + - + +
97V ALA 3.2 28.7 - - - -
98V PHE* 3.5 2.9 - - - -
99V ILE* 2.9 53.6 + - + +
116V ILE* 3.6 4.6 - - - +
117V ALA* 1.3 82.5 - - - +
119V LYS* 1.3 84.4 + - - +
120V PRO* 4.4 1.9 - - - +
121V ALA 5.2 0.5 + - - -
----------------------------------------------------------
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