Contacts of the helix formed by residues 97 - 110 (chain B) in PDB entry 3ISL
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 GLY 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.3 13.6 - - - +
96B TYR* 1.3 82.0 - - - +
98B ARG* 1.3 67.6 + - - +
99B PHE 3.2 3.7 + - - -
100B GLY 3.3 8.8 + - - -
101B TYR* 3.7 3.1 - - - -
121B TRP* 3.5 19.7 - - - +
148B GLU* 3.3 15.1 + - - -
150B SER* 3.7 6.7 - - - -
151B THR* 3.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASN* 3.8 21.6 + - - +
74B ARG* 3.2 27.0 - - - +
97B GLY* 1.3 71.2 - - - -
99B PHE* 1.3 90.5 + - - +
101B TYR* 3.2 24.8 + - + +
102B LEU* 3.6 20.4 + - - +
121B TRP* 3.5 20.1 - - + -
150B SER* 2.9 26.8 + - - +
356B PHE 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASN* 4.9 4.7 - - - -
74B ARG* 4.1 16.6 - - - -
98B ARG* 1.3 102.5 - - + +
100B GLY* 1.3 63.0 + - - +
101B TYR 3.2 0.2 - - - -
102B LEU* 3.4 19.6 + - + +
103B LEU* 3.3 19.6 + - - +
145B VAL* 3.4 17.2 - - + +
148B GLU* 2.9 29.8 + - - +
149B THR* 3.6 21.1 - - - -
150B SER* 4.5 8.7 - - - -
174B ASP* 4.3 1.1 - - - +
365B ARG* 5.9 0.7 - - - -
419B PLP 3.4 64.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.8 2.7 - - - +
94B PRO 5.1 2.2 - - - -
95B ILE* 3.8 24.0 - - - -
97B GLY 3.3 5.7 + - - -
98B ARG 3.3 0.6 - - - -
99B PHE* 1.3 78.3 - - - +
101B TYR* 1.3 59.7 + - - +
103B LEU* 3.2 10.8 + - - +
104B THR* 3.2 24.8 + - - +
145B VAL* 3.5 8.7 - - - +
148B GLU* 2.8 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.5 34.5 - - + +
97B GLY 3.7 9.0 - - - -
98B ARG* 3.2 15.4 + - + +
100B GLY* 1.3 74.1 - - - +
102B LEU* 1.3 61.3 + - - +
104B THR* 2.9 11.5 + - - +
105B GLU* 2.8 30.0 + - - +
116B MET* 4.8 5.4 - - + -
118B GLU* 2.8 37.9 + - - +
121B TRP* 3.7 31.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN* 3.8 28.9 - - - +
74B ARG* 3.7 38.6 - - + +
77B ILE* 4.4 11.9 - - + -
98B ARG* 3.6 20.7 + - - +
99B PHE* 3.4 33.6 + - + +
100B GLY 3.4 0.2 - - - -
101B TYR* 1.3 77.1 - - - +
103B LEU* 1.3 63.7 + - + +
105B GLU* 3.3 6.1 + - + +
106B ILE* 3.0 42.4 + - + +
174B ASP* 5.1 0.7 - - - +
419B PLP 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.6 37.0 - - + -
81B LEU* 4.1 12.3 - - + +
93B ILE* 3.7 16.6 - - + +
99B PHE 3.3 11.4 + - - +
100B GLY* 3.2 8.4 + - - +
101B TYR 3.2 0.6 - - - -
102B LEU* 1.3 78.3 - - + +
104B THR* 1.3 57.4 + - - +
106B ILE* 3.5 5.0 + - - +
107B ALA* 2.9 30.1 + - - +
143B ALA* 3.6 14.4 - - + +
144B MET* 3.5 42.4 - - - +
145B VAL* 4.0 10.8 - - + +
172B ILE* 5.5 1.8 - - + +
174B ASP* 4.8 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.7 24.7 - - + -
95B ILE* 3.4 22.7 - - + -
100B GLY 3.2 14.5 + - - +
101B TYR* 2.9 26.5 + - - +
102B LEU 3.2 0.2 - - - -
103B LEU* 1.3 75.2 - - - +
105B GLU* 1.3 66.1 + - - +
107B ALA* 3.1 2.3 + - - +
108B GLU* 2.8 37.5 + - - +
114B VAL* 4.1 16.4 - - + -
116B MET* 4.3 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 5.6 1.6 - - - +
249A ASN* 4.0 16.6 - - - +
101B TYR 2.8 21.3 + - - +
102B LEU* 3.6 8.7 - - + +
104B THR* 1.3 73.2 + - - +
106B ILE* 1.3 62.1 + - + +
108B GLU* 3.4 12.2 + - - +
109B ARG* 2.8 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN* 4.3 14.1 - - + +
74B ARG* 4.4 5.4 - - + +
77B ILE* 3.9 26.0 - - + -
78B GLU* 4.0 37.2 - - + +
81B LEU* 3.8 22.2 - - + -
102B LEU* 3.0 40.8 + - + +
103B LEU 3.9 3.4 - - - +
105B GLU* 1.3 76.4 - - - +
107B ALA* 1.3 62.5 + - - +
109B ARG* 3.3 5.8 + - - +
110B TYR* 3.1 40.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.9 2.2 - - + +
85B ILE* 3.8 25.8 - - + -
91B VAL* 4.3 4.3 - - + -
93B ILE* 4.0 11.4 - - + -
103B LEU 2.9 19.0 + - - +
104B THR 3.6 2.9 - - - +
106B ILE* 1.3 76.8 - - - +
108B GLU* 1.3 64.0 + - - +
110B TYR* 3.1 12.0 + - - +
111B GLY 3.4 0.2 + - - -
112B ALA* 3.1 22.9 + - + +
114B VAL* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR* 2.8 23.9 + - - +
105B GLU* 3.9 14.2 - - - +
107B ALA* 1.3 75.7 - - - +
109B ARG* 1.3 59.6 + - + +
111B GLY* 2.8 21.1 + - - -
112B ALA 4.3 7.8 - - - +
114B VAL* 3.5 31.5 - - + +
116B MET* 4.8 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 4.3 25.3 - - + +
246A ILE 2.8 28.9 + - - +
247A THR* 3.1 46.4 + - - +
248A SER 3.7 0.2 + - - -
249A ASN* 3.7 21.4 - - - +
252A ASP* 2.9 26.7 + - - -
255A GLN* 3.5 19.0 - - - +
105B GLU* 2.8 55.3 + - - +
106B ILE* 3.6 7.0 - - - +
108B GLU* 1.3 78.5 - - + +
110B TYR* 1.3 58.8 + - - +
111B GLY 3.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 4.6 1.4 + - - -
247A THR* 4.0 20.9 - - + -
248A SER* 4.2 5.0 - - - -
78B GLU* 2.8 43.7 + - + +
81B LEU 5.4 0.2 - - - -
82B ALA* 3.6 32.9 - - + +
85B ILE* 3.7 30.9 - - + +
86B GLU 4.1 0.3 - - - -
87B PRO* 3.9 14.7 - - - +
106B ILE* 3.1 31.3 + - + +
107B ALA 3.1 6.9 + - - +
109B ARG* 1.3 78.5 - - - +
111B GLY* 1.3 59.1 + - - +
112B ALA 3.5 2.9 + - - -
247B THR* 3.7 34.3 - - + -
248B SER* 3.5 23.6 - - - -
----------------------------------------------------------
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