Contacts of the strand formed by residues 21 - 28 (chain H) in PDB entry 2FRV
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 LEU 21 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASP* 4.4 1.9 - - - +
13H PRO* 4.0 7.4 - - - +
14H ILE* 3.3 28.8 + - + +
17H ILE* 3.5 22.3 - - + +
19H GLY 3.6 3.4 + - - -
20H HIS* 1.3 74.1 - - - +
22H ARG* 1.3 68.3 + - - +
23H ILE* 4.1 17.9 - - + -
37H SER* 3.7 20.6 - - - +
38H MET 3.4 24.9 - - - +
39H SER* 4.1 9.4 - - - +
40H THR* 5.1 1.8 - - - -
490H LEU* 3.8 23.3 - - + -
524H VAL* 4.1 15.7 - - + -
529H PRO* 4.6 0.4 - - + -
531H ILE* 3.7 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLU 3.3 23.2 + - - -
196E ALA* 3.4 16.7 + - - +
88G GLY 4.1 12.9 + - - -
10H VAL* 3.8 12.5 - - + +
11H VAL 3.5 4.3 - - - -
12H ASP* 3.1 41.1 + - + +
21H LEU* 1.3 75.6 - - - +
23H ILE* 1.3 62.7 + - - +
24H GLU* 2.7 34.6 + - + -
38H MET* 2.7 57.6 + - - +
40H THR* 4.1 3.8 - - + -
348H PHE* 3.5 33.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE 3.8 0.7 - - - +
10H VAL* 3.2 3.6 - - - +
11H VAL* 2.6 40.7 + - + +
14H ILE* 3.4 33.0 - - + -
21H LEU* 4.1 15.0 - - + -
22H ARG* 1.3 77.1 - - - +
24H GLU* 1.3 65.5 - - - +
25H VAL* 3.7 24.2 - - + -
36H TRP 3.8 3.8 - - - +
37H SER* 4.3 20.0 - - - +
502H VAL* 5.1 4.7 - - + -
506H LEU* 3.9 16.2 - - + -
520H ILE* 4.0 12.8 - - + -
524H VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ALA* 4.7 2.9 - - - +
8H LYS* 4.6 12.8 - - + +
9H ILE 3.4 6.1 - - - +
10H VAL* 4.2 11.0 - - + -
22H ARG* 2.7 37.3 + - - +
23H ILE* 1.3 76.3 - - - +
25H VAL* 1.3 65.1 + - - +
36H TRP* 3.0 46.3 + - + +
38H MET* 3.4 22.6 - - - +
348H PHE* 4.8 0.7 - - - -
349H HIS* 2.6 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LYS* 2.9 12.4 - - - +
9H ILE* 2.8 63.3 + - + +
23H ILE* 3.7 21.1 - - + -
24H GLU* 1.3 78.8 - - - +
26H GLU* 1.3 59.5 + - - +
27H VAL* 3.8 13.9 - - + -
32H ILE* 4.1 13.2 - - + -
34H ASN 3.5 8.7 - - - +
35H ALA* 4.0 6.5 - - + -
36H TRP* 4.2 2.7 - - - -
506H LEU* 4.0 16.4 - - + -
520H ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ASN 3.3 6.7 - - - +
8H LYS* 3.1 31.5 + - - +
25H VAL* 1.3 73.7 - - - +
27H VAL* 1.3 59.8 + - - +
32H ILE* 3.5 4.0 - - - -
33H LYS* 2.7 70.9 + - + +
34H ASN* 3.2 19.3 + - + +
36H TRP* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ASN 2.7 29.7 + - - +
9H ILE* 3.8 31.6 - - + -
25H VAL* 3.8 14.8 - - + -
26H GLU* 1.3 82.5 - - - +
28H GLU* 1.3 65.6 + - - +
30H GLY* 3.8 13.7 - - - +
31H LYS 3.4 24.7 - - - +
32H ILE* 4.5 6.5 - - + -
33H LYS* 4.8 0.7 - - - +
511H ILE* 4.5 13.0 - - + -
514H PRO* 6.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H VAL* 1.3 77.8 - - - +
29H GLY* 1.3 65.4 + - - +
31H LYS* 3.1 20.8 + - + +
33H LYS* 3.6 40.8 - - + +
----------------------------------------------------------
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