Contacts of the strand formed by residues 97 - 103 (chain A) 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 TYR 97 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 3.4 4.0 - - - -
42A VAL* 2.7 44.9 + - + +
44A PRO* 4.3 9.4 - - + -
50A PRO* 3.9 35.6 - - + +
87A ILE* 4.0 24.9 - - + -
88A GLU 3.4 7.2 - - - +
89A PRO* 3.8 27.4 - - + -
90A VAL* 3.8 7.3 - - - +
95A ASN* 3.6 36.8 + - - -
96A GLN* 1.3 82.6 - - - +
98A ILE* 1.3 60.1 + - - +
99A CYS* 3.9 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.4 9.6 - - + -
40A PHE 3.2 6.1 - - - +
41A ARG* 4.0 31.0 - - + +
86A HIS 3.9 0.7 - - - +
87A ILE* 3.5 3.5 - - - -
88A GLU* 2.8 50.9 + - + +
89A PRO 5.2 1.3 - - - +
90A VAL* 3.9 19.5 - - + -
97A TYR* 1.3 74.1 - - - +
99A CYS* 1.3 60.5 + - - +
100A TYR* 3.6 30.0 - - + +
136A GLU* 4.9 1.8 - - + -
358A ARG* 4.3 9.6 - - - +
363A TYR* 4.1 27.4 - - + +
----------------------------------------------------------
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 ALA 3.6 1.7 - - - +
39A ALA* 3.8 0.2 - - - -
40A PHE* 2.8 38.6 + - + +
42A VAL* 3.7 32.5 - - + -
50A PRO* 4.4 7.0 - - - -
54A GLY* 4.0 17.5 - - - -
57A VAL* 6.4 0.7 - - + -
84A CYS* 4.1 13.5 - - - -
86A HIS 3.5 3.8 - - - -
87A ILE* 4.0 23.8 - - - -
97A TYR* 4.4 6.1 - - - -
98A ILE* 1.3 76.3 - - - +
100A TYR* 1.3 63.0 + - - +
101A VAL* 3.8 4.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 3.4 4.0 - - - +
39A ALA* 4.3 9.9 - - + -
84A CYS* 3.2 5.4 - - - -
85A TYR* 3.0 52.0 + + + +
86A HIS* 2.8 47.5 + + + +
88A GLU* 3.1 26.8 + - + -
98A ILE* 3.6 20.1 - - + +
99A CYS* 1.3 74.4 - - - +
101A VAL* 1.3 60.7 - - - +
356A LYS* 5.5 5.8 + - - -
358A ARG* 3.3 14.6 + - - -
363A TYR* 3.8 15.3 + + + +
364A PHE* 3.7 35.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE 3.8 0.9 - - - +
37A LEU* 3.4 2.9 - - - -
38A ALA* 2.8 39.1 + - - +
40A PHE* 4.0 22.4 - - + -
54A GLY 4.6 4.7 - - - +
57A VAL* 4.9 1.1 - - + -
58A ALA* 3.7 27.6 - - + +
83A ARG 3.2 14.1 - - - +
84A CYS* 4.2 12.8 - - + -
85A TYR* 3.7 3.9 - - - -
99A CYS* 4.3 6.1 - - + +
100A TYR* 1.3 79.9 - - - +
102A ALA* 1.3 62.2 + - - +
103A TYR* 3.6 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.8 29.2 - - + -
35A ASP* 4.1 5.8 - - - +
36A ILE 3.5 4.5 - - - -
37A LEU* 3.7 20.9 - - + -
82A GLY* 3.2 5.9 - - - -
83A ARG* 2.9 35.1 + - + +
85A TYR* 3.7 10.5 - - + -
101A VAL* 1.3 74.3 - - - +
103A TYR* 1.3 61.6 + - - +
104A PRO* 4.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 3.4 5.2 - - - -
36A ILE* 2.8 58.0 + - + +
38A ALA* 3.9 20.4 - - + -
40A PHE* 3.6 21.3 - - - -
57A VAL 4.4 0.5 + - - -
58A ALA 4.5 1.1 - - - -
61A SER* 2.7 48.2 + - - -
62A SER* 4.3 7.9 - - - -
82A GLY* 4.3 1.1 - - - -
101A VAL* 3.6 23.0 - - + +
102A ALA* 1.3 77.4 - - - +
104A PRO* 1.3 68.4 - - + +
107A LEU* 4.2 13.7 - - + -
108A PHE* 3.6 25.4 - + + -
119A SER* 5.9 0.2 - - - -
120A ILE* 4.1 19.1 - - + +
----------------------------------------------------------
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