Contacts of the strand formed by residues 89 - 95 (chain E) in PDB entry 3VI4
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 89 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU* 4.0 4.7 - - - -
43E GLN 3.6 11.4 - - - -
44E ARG* 4.6 1.3 - - - -
45E PRO* 4.6 7.6 - - - -
87E ASP 3.5 3.8 + - - -
88E VAL* 1.3 76.3 - - - +
90E ILE* 1.3 64.5 + - - -
91E TYR* 3.9 3.9 - - - -
107E THR 3.7 0.2 - - - +
108E LYS* 3.5 4.1 - - - +
109E LEU* 2.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE 3.8 0.5 - - - +
42E LEU* 3.4 1.9 - - - -
43E GLN* 2.7 51.9 + - + +
89E GLY* 1.3 77.0 - - - +
91E TYR* 1.3 62.5 + - - +
92E PHE* 3.7 27.3 + - + -
106E GLY* 3.7 25.8 - - - -
107E THR 3.5 9.4 - - - +
108E LYS* 4.3 25.8 - - + +
39F GLN* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 2.8 23.6 + - - -
21E ILE* 4.0 14.8 - - + -
40E TRP* 4.4 9.6 - - + -
41E PHE 3.3 3.8 - - - +
42E LEU* 3.5 30.4 - - + +
52E LEU* 3.7 18.8 - - + -
67E PHE* 3.8 8.0 - + - -
78E LEU* 3.6 18.4 - - + -
80E ILE* 3.8 20.7 - - + +
87E ASP* 2.6 44.9 + - - +
89E GLY 3.9 7.2 - - - -
90E ILE* 1.3 75.3 - - - +
92E PHE* 1.3 62.3 + - - +
106E GLY* 3.4 0.3 - - - -
107E THR* 2.9 34.0 + - - +
109E LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.7 1.1 - - - -
40E TRP* 3.4 7.8 - - - -
41E PHE* 2.7 48.3 + - + +
43E GLN* 3.7 27.6 - - + -
49E PRO* 5.6 0.4 - - + -
90E ILE* 3.7 35.2 - - + -
91E TYR* 1.3 74.5 - - - +
93E CYS* 1.3 64.6 + - - +
103E PHE* 4.2 11.7 - - + -
104E GLY 3.5 20.0 - - - -
106E GLY* 3.4 21.8 - - - -
39F GLN* 5.4 1.3 - - - -
44F GLY* 4.1 13.0 - - - -
45F LEU* 3.6 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E MET* 4.3 2.7 - - - -
6E GLN* 3.2 24.3 + - - -
23E CYS* 2.0 52.5 - - + -
38E LEU* 4.0 6.3 - - + -
39E TYR 3.3 12.6 - - - +
40E TRP* 4.3 9.9 - - + -
41E PHE* 4.8 0.4 - - - -
92E PHE* 1.3 75.5 - - - +
94E LEU* 1.3 64.0 + - - +
103E PHE* 3.3 26.9 - - - +
104E GLY 3.6 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E MET* 4.6 2.2 - - - -
38E LEU* 3.4 9.7 - - - +
39E TYR* 2.9 37.0 + - + -
41E PHE* 3.5 23.8 - - + -
93E CYS* 1.3 78.9 - - - +
95E GLN* 1.3 75.5 + - - +
96E HIS* 3.6 20.4 - - + +
101E PHE* 3.9 11.2 - - + -
102E THR 3.3 37.0 - - - +
103E PHE* 3.5 31.9 - - + -
104F ALA* 5.7 1.1 - - + -
105F MET* 5.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ILE* 3.4 26.5 - - + +
4E MET* 3.7 24.2 - - - -
29E LEU* 3.8 20.0 - - + -
37E TYR 3.8 4.7 - - - +
94E LEU* 1.3 80.0 - - - +
96E HIS* 1.3 58.1 + - - +
97E LEU* 3.2 2.9 + - - +
98E GLU 3.0 30.3 + - - -
100E PRO 2.9 29.1 + - - -
101E PHE* 3.2 10.5 - - - +
102E THR* 3.0 34.8 + - - +
----------------------------------------------------------
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