Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 1ISR
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 HIS 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 4.3 14.1 - - + -
57A PRO* 3.9 25.8 - - + -
62A VAL* 3.5 33.0 - - + +
108A SER 3.2 5.7 + - - +
109A CYS 3.9 7.0 - - - +
110A TRP* 1.3 78.1 - - - +
112A SER* 1.3 64.4 + - - +
113A SER* 3.0 42.1 + - - -
114A VAL* 4.4 6.5 - - + -
115A ALA* 2.9 31.6 + - - +
167A VAL* 4.0 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 1.3 77.1 + - - +
113A SER* 1.3 57.6 + - - +
115A ALA* 4.3 0.2 - - - -
116A LEU* 3.1 29.4 + - - +
166A SER* 3.5 25.6 + - - -
167A VAL* 3.6 20.7 - - - +
170A GLN* 3.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.6 7.3 + - - +
65A ARG* 3.4 28.5 + - - +
111A HIS* 3.0 25.0 + - - -
112A SER* 1.3 77.2 - - - +
114A VAL* 1.3 61.4 + - - +
116A LEU* 3.2 7.6 + - - +
117A GLU* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.4 12.1 - - + -
65A ARG* 4.1 26.9 - - + +
67A CYS* 4.2 16.8 - - - -
107A ASP* 4.2 10.3 - - + +
108A SER 3.6 12.1 - - - +
109A CYS* 4.0 23.3 - - + -
111A HIS* 3.3 7.9 + - + +
113A SER* 1.3 73.3 - - - +
115A ALA* 1.3 65.0 + - - +
117A GLU* 3.0 27.5 + - - +
118A GLN* 3.0 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.4 6.0 - - + +
108A SER* 3.8 22.3 + - - +
111A HIS 2.9 19.0 + - - +
112A SER 4.2 2.2 - - - +
114A VAL* 1.3 77.4 - - - +
116A LEU* 1.3 51.6 + - - +
118A GLN* 3.7 5.6 + - - +
119A SER* 2.8 34.9 + - - -
167A VAL* 3.4 26.5 - - + -
171A VAL* 4.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER 3.1 19.6 + - - +
113A SER* 3.5 7.2 - - - +
114A VAL 3.1 0.8 - - - -
115A ALA* 1.3 73.6 - - - +
117A GLU* 1.3 62.9 + - - +
118A GLN 3.2 0.7 - - - -
119A SER* 3.4 4.0 + - - +
120A ILE* 3.0 36.0 + - + +
170A GLN* 4.0 43.7 - - + +
171A VAL* 5.1 1.5 - - - +
174A LEU* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 5.1 14.7 + - - -
65A ARG* 3.1 40.5 + - - +
113A SER 3.0 12.6 + - - +
114A VAL* 3.0 19.2 + - - +
116A LEU* 1.3 77.8 - - - +
118A GLN* 1.3 74.7 + - - +
120A ILE* 3.5 20.3 - - - +
121A GLU* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 4.0 23.9 + - - +
37A SER 5.3 0.7 - - - +
38A VAL* 4.9 1.9 - - - +
50A LEU* 4.3 6.7 - - + -
106A ARG* 3.2 46.9 + - + +
107A ASP* 3.2 26.8 + - - +
114A VAL* 3.0 17.2 + - + +
115A ALA 4.0 4.7 - - - +
117A GLU* 1.3 93.3 + - - +
119A SER* 1.3 64.6 + - - +
120A ILE 3.1 2.0 - - - -
121A GLU* 3.0 25.8 + - - +
122A PHE* 3.3 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.2 3.8 - - - +
115A ALA 2.8 22.8 + - - -
116A LEU* 3.8 7.1 - - - -
117A GLU 3.4 0.4 - - - -
118A GLN* 1.3 76.4 - - - +
120A ILE* 1.3 62.2 + - - +
122A PHE* 3.0 30.7 + - - +
123A ILE* 3.3 10.9 - - - +
171A VAL* 3.4 29.5 - - - +
174A LEU* 3.7 21.9 - - - +
175A LEU* 5.3 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.0 21.5 - - + +
117A GLU* 3.5 13.0 - - - +
119A SER* 1.3 78.8 - - - +
121A GLU* 1.3 68.5 + - - +
123A ILE* 3.1 19.4 - - + +
124A ARG* 3.1 29.2 + - + +
174A LEU* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 6.3 0.2 - - - +
104A GLU* 4.6 1.6 - - - +
106A ARG* 3.4 37.0 + - - +
117A GLU* 3.7 18.1 - - + +
118A GLN* 3.0 20.8 + - - +
120A ILE* 1.3 81.2 - - - +
122A PHE* 1.3 62.3 + - - +
123A ILE 3.2 0.5 + - - -
124A ARG* 3.2 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.8 12.3 - - - -
49A ALA 3.9 12.8 - - - -
50A LEU* 3.5 33.0 - - + -
104A GLU* 3.4 40.6 - - + -
106A ARG* 3.5 24.0 - - + -
118A GLN 3.3 12.8 + - - -
119A SER* 3.0 19.8 + - - +
121A GLU* 1.3 78.4 - - - +
123A ILE* 1.3 66.2 + - + +
124A ARG 4.0 0.9 + - - +
155A PRO* 5.9 0.5 - - - +
156A ILE* 3.8 35.3 + - + +
159A VAL* 4.6 14.4 - - + -
171A VAL* 6.2 0.4 - - + -
175A LEU* 5.1 8.3 - - + -
180A ILE* 5.5 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER 3.3 14.4 - - - +
120A ILE* 3.1 39.0 - - + +
122A PHE* 1.3 84.4 - - + +
124A ARG* 1.3 62.3 + - - +
174A LEU* 4.5 11.2 - - + -
175A LEU* 4.8 6.7 - - + -
178A PHE* 3.9 53.0 - - + -
180A ILE* 3.9 20.6 - - + -
----------------------------------------------------------
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