Contacts of the helix formed by residues 117 - 125 (chain A) in PDB entry 6V96
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 ASN 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 2.9 21.7 + - + +
95A LEU* 3.7 27.4 - - + +
96A PRO 5.4 0.9 - - - +
100A ARG* 3.2 23.2 + - - -
107A TYR* 3.0 26.1 + - - -
113A ALA 2.9 24.5 + - - -
114A VAL 2.7 14.9 + - - +
116A GLN* 1.3 73.2 - - - +
118A ILE* 1.3 62.5 + - - +
119A ASP* 3.1 8.1 - - - -
120A ILE* 2.9 16.4 + - + +
121A ILE* 3.3 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL 3.4 2.7 + - - +
115A TYR* 3.1 51.9 + - + +
116A GLN 3.6 0.4 - - - -
117A ASN* 1.3 77.2 - - - +
119A ASP* 1.3 57.2 + - - +
121A ILE* 3.0 8.9 + - + +
122A GLU* 2.9 60.4 + - + +
217A MET* 3.7 31.0 - - + +
220A LEU* 4.6 3.4 - - + -
221A ARG* 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.5 28.9 + - - -
101A VAL* 4.2 18.2 - - - +
116A GLN 3.8 3.8 - - - +
117A ASN* 3.6 11.1 - - - -
118A ILE* 1.3 74.0 - - - +
120A ILE* 1.3 64.4 + - - +
122A GLU* 5.1 4.7 - - - -
123A PRO* 3.1 23.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
14A MET* 5.1 4.0 - - + -
93A ASP* 3.8 36.3 - - + +
95A LEU* 4.0 25.6 - - + -
100A ARG* 4.0 18.8 - - - +
117A ASN* 2.9 15.7 + - + +
119A ASP* 1.3 93.5 + - - +
121A ILE* 1.3 65.2 + - + +
123A PRO* 3.6 8.5 - - - +
124A TYR* 3.4 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.9 19.7 - - + -
16A TYR* 4.1 9.6 - - + -
114A VAL* 3.9 28.5 - - + -
117A ASN 3.6 15.9 - - - +
118A ILE* 3.0 8.8 + - - +
120A ILE* 1.3 79.4 - - + +
122A GLU* 1.3 68.2 + - + +
124A TYR* 2.9 23.2 + - - +
125A ALA 3.1 8.0 + - - -
126A PRO* 3.8 25.1 - - + -
129A MET* 3.9 21.3 - - + -
213A THR* 4.2 11.0 - - + -
217A MET* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 2.9 32.8 + - + +
119A ASP* 5.1 2.9 - - - -
121A ILE* 1.3 78.2 - - + +
123A PRO* 1.3 62.4 - - + +
125A ALA* 2.8 27.3 + - - +
213A THR* 6.4 0.7 - - + -
217A MET* 4.6 12.4 - - + +
221A ARG* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 3.1 26.0 - - - +
120A ILE 3.6 6.3 - - - +
121A ILE 3.5 2.9 - - - -
122A GLU* 1.3 93.2 - - + +
124A TYR* 1.3 66.3 + - + +
125A ALA* 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 4.3 16.8 - - + -
61A ARG* 3.4 53.4 + - - +
86A PRO* 6.5 1.3 - - + -
91A SER* 3.5 17.8 - - - -
93A ASP* 2.6 37.8 + - - -
120A ILE* 3.4 28.2 - - + +
121A ILE 2.9 8.4 + - - +
123A PRO* 1.3 81.5 - - + +
125A ALA* 1.3 70.6 + - - +
126A PRO* 3.3 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE 3.1 0.6 + - - -
122A GLU* 2.8 20.0 + - - +
123A PRO 4.5 2.5 - - - +
124A TYR* 1.3 79.8 - - - +
126A PRO* 1.3 73.6 - - - +
127A GLU* 3.6 2.3 + - - +
213A THR* 5.9 0.9 - - - -
----------------------------------------------------------
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