Contacts of the strand formed by residues 115 - 122 (chain F) in PDB entry 2CVL
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 VAL 115 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ILE* 3.9 0.9 - - - -
33F PRO* 3.3 20.3 - - + +
45F ILE* 3.8 10.8 - - + -
48F GLN* 3.9 21.7 - - + +
49F THR* 3.8 16.4 - - - +
52F VAL* 3.8 21.7 - - + +
76F PHE 3.4 6.1 - - - +
77F LEU* 3.9 6.5 - - + -
86F PHE* 3.7 32.3 - - + -
109F LEU* 3.6 3.4 - - - -
113F VAL* 3.5 6.6 - - - +
114F ARG* 1.3 82.7 - - - +
116F GLU* 1.3 65.1 + - - +
117F VAL* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ALA* 3.4 12.9 - - + +
103D THR 2.6 45.7 + - - +
104D VAL* 4.4 5.2 - - - -
30F GLY* 3.6 20.9 - - - +
31F GLN 3.2 11.0 - - - +
32F ILE* 4.0 9.6 - - + -
74F THR 3.8 1.2 - - - +
75F CYS* 3.7 0.9 - - - -
76F PHE* 2.9 38.3 + - + +
109F LEU* 3.6 18.5 - - + +
110F PRO* 3.3 16.7 - - - +
115F VAL* 1.3 75.7 - - - +
117F VAL* 1.3 65.5 + - - +
118F ALA 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F GLY* 3.8 0.9 - - - -
31F GLN* 2.8 32.4 + - - +
52F VAL* 3.7 22.0 - - + +
53F MSE 4.7 5.4 - - - -
56F LEU* 3.4 31.0 - - + +
73F THR* 4.3 8.3 - - + -
74F THR 3.5 2.0 - - - -
75F CYS* 4.0 17.5 - - + -
86F PHE* 3.8 34.8 - - + -
90F TYR* 4.9 2.2 - - + -
115F VAL* 4.0 2.2 - - + -
116F GLU* 1.3 79.3 - - - +
118F ALA* 1.3 70.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN* 6.1 3.1 - - - +
101D ARG 5.7 0.2 - - - -
102D ALA* 4.2 17.3 - - + -
28F VAL 3.4 16.2 - - - +
29F SER* 3.8 1.1 - - - -
30F GLY* 3.6 17.0 - - - +
56F LEU* 4.8 0.2 - - - -
73F THR* 3.3 1.9 - - - -
74F THR* 2.9 40.4 + - - +
76F PHE* 5.8 0.9 - - + -
116F GLU* 4.3 0.6 - - - +
117F VAL* 1.3 79.0 - - - +
119F CYS* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN* 5.0 2.4 + - - -
27F PHE* 3.8 0.3 - - - -
28F VAL* 2.8 56.7 + - - +
56F LEU* 4.1 16.4 - - + -
60F LEU* 4.1 6.7 - - - -
70F VAL* 4.0 23.6 - - + -
72F GLN* 3.1 17.0 - - - +
73F THR* 3.9 13.7 - - + +
74F THR* 4.8 0.9 - - - +
117F VAL* 5.3 0.4 - - + -
118F ALA* 1.3 78.9 - - - +
120F VAL* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN* 3.8 11.4 - - - +
27E PHE* 4.3 11.2 - - + -
25F PHE* 3.8 34.1 - - + -
26F VAL 3.4 4.7 - - - +
27F PHE* 3.8 27.1 - - + -
70F VAL* 3.7 1.7 - - - +
71F VAL* 2.9 28.6 + - + +
72F GLN* 2.8 40.5 + - + +
119F CYS* 1.3 79.9 - - - +
121F ALA* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F PHE* 3.2 12.0 - - - +
26F VAL* 2.7 36.1 + - + +
60F LEU* 3.6 29.2 - - + -
65F SER* 3.7 8.7 - - - +
69F ARG 3.3 17.0 - - - +
70F VAL* 3.6 11.0 - - + -
71F VAL* 4.0 2.2 - - - +
119F CYS* 5.0 0.2 - - - -
120F VAL* 1.3 75.0 - - - +
122F LEU* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MSE 3.6 30.5 - - + -
22E ALA* 3.9 7.4 - - + -
23E GLY* 4.0 19.5 - - - +
24F GLY 3.8 8.7 - - - +
25F PHE* 3.8 22.7 - - + -
26F VAL* 4.4 0.7 - - - -
65F SER* 2.9 22.7 + - - -
69F ARG* 2.9 36.0 + - + +
71F VAL* 4.0 9.6 - - + -
121F ALA* 1.3 72.4 - - - +
123F ALA* 1.3 60.5 + - - +
124F GLU* 3.4 14.2 + - - +
----------------------------------------------------------
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