Contacts of the strand formed by residues 98 - 105 (chain T) 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 PHE 98 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T TYR* 3.5 38.8 - + - -
44T PHE* 3.2 6.2 - - - +
45T GLU 2.9 37.0 + - - +
46T THR 5.7 5.2 - - - -
49T GLY* 4.0 25.4 - - - -
50T PHE* 4.5 7.0 - + - -
67T TRP* 3.5 25.9 - + + -
96T ASN 5.5 0.7 - - - -
97T ALA* 1.3 74.4 - - - +
99T ILE* 1.3 58.6 + - - +
116T ILE* 5.1 2.5 - - + -
118T TYR 3.5 5.2 - - - +
119T LYS* 4.1 11.4 - - + -
120T PRO* 3.7 24.2 - - + -
123T TYR* 3.7 39.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T LEU* 4.6 9.4 - - + -
43T GLU 3.4 9.2 - - - +
44T PHE* 4.3 4.3 - - + -
67T TRP* 4.4 1.3 - - - -
87T LEU* 3.7 19.7 - - + -
90T CYS* 3.7 32.3 - - + +
91T LYS* 3.5 39.5 - - + +
94T TYR 4.4 4.5 - - - +
97T ALA* 4.0 4.9 - - + +
98T PHE* 1.3 77.3 - - - +
100T ARG* 1.3 67.8 + - - +
116T ILE* 3.6 4.0 - - - +
117T ALA* 2.8 25.9 + - + -
118T TYR* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASN* 4.0 23.0 + - - +
183C LYS* 6.0 0.8 - - - +
41T CYS 3.8 0.3 - - - +
42T LEU* 3.4 7.3 - - - +
43T GLU* 2.8 64.3 + - + +
64T GLY 5.6 0.2 + - - -
65T ARG 3.4 15.2 + - - -
66T TYR* 5.1 0.2 - - - +
67T TRP* 3.2 63.4 - - + +
99T ILE* 1.3 76.0 - - - +
101T ILE* 1.3 64.6 + - - +
102T ILE* 3.9 13.9 - - + +
111T GLN* 6.4 0.2 - - - -
114T SER* 3.7 18.6 - - - +
115T PHE 3.7 13.0 - - - +
116T ILE* 4.3 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T LEU* 4.5 5.4 - - + -
30T VAL* 4.6 13.2 - - + -
33T LEU* 4.3 17.9 - - + -
40T PRO* 5.5 0.2 - - + -
41T CYS 3.6 7.0 - - - +
42T LEU* 4.5 14.8 - - + -
83T VAL* 4.6 19.5 - - + -
84T LEU* 5.8 1.3 - - + -
87T LEU* 4.4 15.7 - - + -
100T ARG* 1.3 77.2 - - - +
102T ILE* 1.3 69.7 + - - +
113T VAL 4.3 0.2 - - - -
114T SER* 3.3 4.2 + - - -
115T PHE* 3.1 57.9 + - + +
117T ALA* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T LEU* 4.0 8.2 - - - +
39T VAL 4.4 0.2 - - - -
40T PRO* 3.4 4.0 - - - +
41T CYS* 2.9 50.2 + - + +
43T GLU* 3.8 33.7 - - + +
100T ARG* 3.9 13.2 - - + -
101T ILE* 1.3 80.5 - - - +
103T GLY* 1.3 60.9 + - - +
104T PHE* 3.5 31.6 - - + -
111T GLN* 3.8 25.1 - - - +
113T VAL 3.2 8.5 - - - +
114T SER* 3.8 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T LEU* 4.2 17.9 - - - -
38T TRP* 4.3 4.9 - - - -
39T VAL 3.3 9.4 - - - -
102T ILE* 1.3 76.8 - - - +
104T PHE* 1.3 63.0 + - - -
111T GLN* 3.3 4.9 - - - -
112T CYS* 2.9 28.8 + - - +
113T VAL* 3.0 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ASN* 4.1 13.5 - - - -
187C ARG* 3.7 33.4 - - - -
37T LYS 4.7 0.2 - - - +
38T TRP* 3.2 10.6 - - - -
39T VAL* 2.8 55.6 + - + +
41T CYS* 3.8 26.2 - - + -
69T MET* 5.4 0.2 - - + -
73T PRO* 4.1 22.4 - - + -
75T PHE* 6.1 0.9 - + - -
102T ILE* 3.5 17.3 - - + -
103T GLY* 1.3 73.2 - - - -
105T ASP* 1.3 62.3 + - - +
106T SER* 3.7 5.8 + - - +
109T GLN 6.1 1.3 - - - -
110T VAL 4.0 3.6 - - - -
111T GLN* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T LYS 5.9 0.2 - - - -
38T TRP* 3.3 23.8 + - + -
104T PHE* 1.3 72.4 - - - +
106T SER* 1.3 52.7 + - - +
107T ASN* 3.1 23.2 + - - +
108T ARG* 3.3 22.9 + - - +
109T GLN* 2.7 36.2 + - - -
110T VAL* 3.0 20.6 + - + +
112T CYS* 3.6 20.4 - - - -
----------------------------------------------------------
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