Contacts of the helix formed by residues 112 - 123 (chain A) in PDB entry 2XVA
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 THR 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 3.4 26.0 - - - +
88A ASN* 2.7 37.8 + - - +
108A LEU* 4.4 7.0 - - + -
109A GLU* 3.0 17.9 + - - +
111A LYS* 1.3 81.3 + - - +
113A ILE* 1.3 65.5 + - - +
114A PRO 3.5 0.2 - - - -
115A GLY* 3.4 3.8 + - - -
116A LEU* 3.0 34.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.9 30.3 - - + +
108A LEU* 4.1 18.6 - - + -
109A GLU 3.9 2.7 - - - +
110A ALA 3.3 5.8 + - - +
112A THR* 1.3 76.8 - - + +
114A PRO* 1.4 73.2 - - + +
116A LEU* 3.3 4.5 + - + +
117A ILE* 3.0 47.0 + - + +
149A PHE* 3.5 58.6 - - + -
151A PHE* 4.5 1.1 - - + -
159A TYR* 3.8 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 3.5 11.2 - - - +
111A LYS 4.0 7.2 - - - +
112A THR 3.7 2.5 - - - -
113A ILE* 1.4 93.1 - - + +
115A GLY* 1.3 56.7 + - - +
117A ILE* 4.0 1.9 - - - +
118A ALA* 3.1 29.0 + - - +
159A TYR* 3.4 28.9 - - + +
158D ARG* 6.3 1.1 - - + -
161D GLU* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS 5.1 1.4 + - - -
112A THR 3.4 5.0 + - - -
113A ILE 3.3 0.4 - - - -
114A PRO* 1.3 76.9 - - - +
116A LEU* 1.3 60.1 + - - +
118A ALA* 3.6 5.3 + - - +
119A ASN* 2.9 29.2 + - - +
122A ARG* 4.8 2.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
37A LEU* 4.2 16.4 - - + -
87A LEU* 4.6 20.6 - - + +
90A LEU* 5.5 7.9 - - + +
92A PHE* 3.9 24.7 - - + -
105A LEU* 3.8 17.7 - - + -
108A LEU* 3.7 31.0 - - + -
112A THR* 3.0 27.1 + - + +
113A ILE* 3.8 4.7 - - + +
115A GLY* 1.3 73.6 - - - +
117A ILE* 1.3 60.6 + - + +
119A ASN* 3.1 6.1 + - + +
120A MET* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.8 6.5 - - + -
113A ILE* 3.0 39.7 + - + +
114A PRO 4.0 2.5 - - - +
116A LEU* 1.3 73.3 - - + +
118A ALA* 1.3 68.1 + - - +
120A MET* 3.2 17.7 + - - +
121A GLN* 2.9 36.9 + - - +
132A ILE* 4.8 5.4 - - + -
151A PHE* 4.0 14.4 - - + -
156A LEU* 4.8 4.7 - - + -
159A TYR* 3.6 42.2 - - + -
160A TYR* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PRO 3.1 18.9 + - - +
115A GLY* 3.8 7.4 - - - +
117A ILE* 1.3 77.8 - - - +
119A ASN* 1.3 56.1 + - - +
121A GLN* 3.3 12.5 + - - +
122A ARG* 3.0 44.2 + - - +
159A TYR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 4.3 2.8 - - - +
91A THR* 3.5 13.3 + - - +
92A PHE* 2.9 60.5 + - + -
115A GLY 2.9 18.8 + - - +
116A LEU* 3.1 8.7 + - + +
118A ALA* 1.3 74.3 - - - +
120A MET* 1.3 64.6 + - - +
122A ARG* 3.4 26.9 + - - +
123A CYS* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.8 28.3 - - + -
92A PHE* 3.9 10.3 - - + -
99A ILE* 3.4 30.9 - - + +
101A SER* 4.7 11.0 - - - +
105A LEU* 5.3 3.8 - - - -
116A LEU* 2.8 29.3 + - + +
117A ILE* 3.3 19.1 - - - +
119A ASN* 1.3 72.7 - - - +
121A GLN* 1.3 55.0 + - - +
123A CYS 3.3 1.4 + - - -
124A THR* 2.7 32.6 + - - -
130A ASN* 3.9 13.9 - - + +
132A ILE* 3.6 36.1 - - + -
160A TYR* 4.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 2.9 27.7 + - - +
118A ALA* 3.3 12.0 + - - +
120A MET* 1.3 73.2 - - - +
122A ARG* 1.3 59.2 + - - +
124A THR* 3.2 10.6 + - - -
159A TYR* 3.0 28.5 + - - +
160A TYR* 3.5 38.6 - - - +
163A TRP* 3.6 32.2 - - + +
196A LYS* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 4.9 9.1 + - - +
92A PHE 5.1 0.8 + - - -
93A ASP* 5.5 4.4 + - - -
95A GLN* 3.2 15.0 + - - +
115A GLY 4.8 1.8 + - - -
118A ALA* 3.0 42.2 + - - +
119A ASN* 3.4 39.6 + - - +
121A GLN* 1.3 77.1 - - - +
123A CYS* 1.3 63.7 + - - +
124A THR 3.5 2.9 + - - +
196A LYS* 3.7 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.5 26.5 - - + -
93A ASP* 3.9 11.0 - - - -
94A ARG 3.1 19.9 - - - +
95A GLN* 3.4 12.2 - - - +
96A TYR* 2.8 30.5 + - + +
99A ILE* 3.9 3.1 - - + +
119A ASN* 3.0 37.6 + - - +
120A MET 3.6 4.0 - - - +
121A GLN 3.1 0.4 - - - -
122A ARG* 1.3 84.6 - - - +
124A THR* 1.3 58.8 + - - +
----------------------------------------------------------
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