Contacts of the helix formed by residues 107 - 118 (chain C) in PDB entry 2VES
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 ALA 107 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS 3.4 22.9 - - - +
81C SER* 4.3 4.3 - - - -
82C ALA* 4.3 8.3 - - + +
106C SER* 1.3 71.0 - - - +
108C GLY* 1.3 63.9 + - - +
109C PRO* 3.4 2.7 - - - -
110C PHE* 3.1 13.7 + - - +
111C VAL* 3.0 22.6 + - - +
181C PHE* 4.4 3.4 - - + -
186C SER* 2.8 19.6 + - - +
240C LEU* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C SER* 3.1 5.4 + - - -
107C ALA* 1.3 76.7 - - - +
109C PRO* 1.3 69.9 - - - +
111C VAL* 3.1 6.1 + - - +
112C PHE* 2.9 35.5 + - - -
186C SER* 3.0 16.8 + - - -
187C ARG* 4.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C MET* 3.8 40.4 - - + -
104C ASP* 3.3 36.6 - - + +
106C SER* 3.5 4.5 - - - +
107C ALA 3.6 2.7 - - - -
108C GLY* 1.3 90.0 - - - +
110C PHE* 1.3 58.8 + - + +
112C PHE* 3.3 15.9 + - + +
113C LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.4 16.4 - - + -
28C LEU* 5.9 0.9 - - + -
78C HIS* 4.0 10.1 - - + -
79C LEU* 3.7 47.6 - - + -
82C ALA* 3.6 15.9 - - + -
100C VAL* 3.8 20.9 - - + -
101C PRO* 3.6 23.8 - - + -
102C ILE 5.0 1.6 - - - -
103C MET* 3.7 22.7 - - + -
106C SER 3.9 13.5 - - - -
107C ALA* 3.1 16.0 + - - +
109C PRO* 1.3 74.2 - - + +
111C VAL* 1.3 67.0 + - - +
113C LEU* 3.2 17.4 + - + +
114C ILE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 3.7 15.9 - - + +
86C LEU* 3.7 15.8 - - + +
107C ALA 3.0 17.1 + - - +
108C GLY* 3.4 9.9 - - - +
110C PHE* 1.3 77.1 - - - +
112C PHE* 1.3 64.2 + - + +
114C ILE* 3.4 2.1 + - - +
115C GLN* 2.9 57.6 + - - +
181C PHE* 3.8 24.0 - - + -
182C VAL* 3.8 17.5 - - + -
186C SER* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLY* 2.9 33.5 + - - -
109C PRO* 3.6 11.4 - - + +
110C PHE 3.2 0.2 - - - -
111C VAL* 1.3 81.3 - - + +
113C LEU* 1.3 58.1 + - + +
115C GLN* 3.5 20.9 + - - +
116C SER* 2.9 29.1 + - - -
186C SER* 6.1 0.4 - - - -
187C ARG* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.6 34.7 - - + +
12C ARG 4.1 2.2 - - - +
13C ALA* 3.7 33.9 - - + -
26C LEU* 4.0 16.4 - - + -
28C LEU* 4.1 13.9 - - + -
103C MET* 5.3 5.2 - - + -
109C PRO* 2.9 23.7 + - + +
110C PHE* 3.2 18.4 + - + +
112C PHE* 1.3 74.6 - - + +
114C ILE* 1.3 58.6 + - - +
116C SER* 3.3 2.8 + - - -
117C ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.8 12.1 - - + -
28C LEU* 4.2 15.5 - - + -
79C LEU* 4.9 2.7 - - + -
82C ALA* 3.8 36.1 - - + +
83C MET* 3.9 25.4 - - + +
86C LEU* 3.5 22.0 - - + -
88C ILE* 3.8 13.9 - - + -
110C PHE 2.9 22.1 + - - +
113C LEU* 1.3 74.6 - - - +
115C GLN* 1.3 56.2 + - - +
117C ALA* 3.2 3.7 + - - +
118C GLY* 3.0 26.0 + - - +
119C LEU* 3.7 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.3 4.9 - - + +
111C VAL* 2.9 33.4 + - - +
112C PHE* 3.5 31.9 - - - +
114C ILE* 1.3 76.0 - - - +
116C SER* 1.3 62.3 + - - +
118C GLY* 3.3 13.7 + - - -
119C LEU* 5.1 0.2 - - - -
182C VAL* 4.5 12.3 - - - +
297C MET* 4.2 25.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 5.1 2.4 + - - +
11C ILE* 3.5 24.4 - - - +
112C PHE 2.9 18.6 + - - -
113C LEU* 3.3 0.9 + - - -
115C GLN* 1.3 74.0 - - - +
117C ALA* 1.3 65.1 + - - +
118C GLY* 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.3 12.8 - - + -
8C LYS* 3.5 0.2 - - - +
9C ASN* 3.0 63.0 + - - +
10C ILE 5.4 0.2 - - - -
11C ILE* 3.8 20.7 - - + +
113C LEU 2.9 16.5 + - - +
114C ILE* 3.2 4.9 + - - +
116C SER* 1.3 76.6 - - - +
118C GLY* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.4 8.5 - - - +
8C LYS* 2.8 33.7 + - - -
9C ASN* 5.2 0.2 - - - -
114C ILE 3.0 9.2 + - - +
115C GLN 3.3 10.5 + - - -
116C SER 3.2 3.9 - - - -
117C ALA* 1.3 77.8 - - - +
119C LEU* 1.3 67.3 + - - +
----------------------------------------------------------
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