Contacts of the strand formed by residues 29 - 36 (chain C) in PDB entry 2VWI
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 29 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY 4.3 0.7 - - - +
25C SER* 3.8 0.7 + - - -
26C GLY* 2.9 33.3 + - - +
27C ALA 3.6 0.8 - - - -
28C THR* 1.3 91.1 - - + +
30C VAL* 1.3 60.8 + - - +
31C VAL 4.2 0.4 + - - -
46C LYS* 3.9 39.7 - - + +
47C ARG 3.5 5.2 - - - +
48C ILE* 4.3 4.9 - - + -
1294C ANP 4.0 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 3.8 25.8 - - + -
24C GLY 3.3 15.7 - - - +
25C SER* 4.6 9.6 - - - +
29C ALA* 1.3 74.1 - - - +
31C VAL* 1.3 63.7 + - - +
32C GLN* 3.9 8.0 + - + +
45C ILE 3.4 2.6 - - - +
46C LYS* 3.4 1.3 - - - -
47C ARG* 2.7 67.0 + - + +
87C GLU* 5.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 3.6 1.7 - - - -
23C ILE* 2.7 48.1 + - + -
24C GLY 2.8 18.4 + - - +
30C VAL* 1.3 73.4 - - - +
32C GLN* 1.3 56.5 + - - +
44C ALA* 4.6 8.7 - - + -
45C ILE 3.4 7.2 - - - +
46C LYS* 3.7 29.8 - - + +
92C MET* 6.2 0.9 - - - -
1294C ANP 3.5 65.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.7 29.6 - - + +
20C GLN 2.9 29.5 + - - +
21C GLU 3.6 7.6 - - - +
22C VAL* 3.8 20.7 - - + +
23C ILE* 4.4 3.1 - - - -
30C VAL* 4.7 4.8 - - + +
31C VAL* 1.3 75.4 - - - +
33C ALA* 1.3 67.8 + - - +
34C ALA* 4.6 0.2 - - - +
45C ILE* 2.8 45.4 + - + +
47C ARG* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 3.6 11.4 - - - +
19C LEU 3.8 0.2 - - - -
20C GLN* 2.8 30.1 + - - -
21C GLU* 2.8 41.9 + - - +
23C ILE* 3.9 8.1 - - + +
32C GLN* 1.3 76.6 - - - +
34C ALA* 1.3 56.2 + - - +
42C LYS* 3.8 11.0 - - - +
43C VAL 3.4 6.5 - - - -
44C ALA* 4.7 0.2 - - - +
94C LEU* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 4.5 7.4 - - + -
18C GLU 3.2 18.8 - - - +
19C LEU* 4.2 6.1 - - + -
20C GLN* 3.8 7.1 + - - -
33C ALA* 1.3 77.5 - - - +
35C TYR* 1.3 58.1 + - - +
42C LYS* 3.4 1.5 - - - +
43C VAL* 2.6 48.1 + - + +
45C ILE* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP 3.6 1.4 - - - +
17C TYR* 3.3 4.3 - - - -
18C GLU* 2.8 42.3 + - + +
20C GLN* 3.7 21.6 + - - +
34C ALA* 1.3 71.7 - - - +
36C CYS* 1.3 58.9 + - - +
37C ALA* 3.7 23.3 - - + -
40C LYS* 3.3 47.7 - - - +
41C GLU* 3.7 13.2 - - - -
42C LYS* 4.0 8.7 - - + +
248D GLU* 6.2 0.2 - - - -
254D LYS* 4.0 14.4 - - + +
255D GLU* 3.5 49.9 - - + +
258D LYS* 4.4 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 3.5 33.2 - - + -
11C SER* 5.0 4.3 - - - -
16C ASP 3.6 5.6 - - - -
17C TYR* 3.6 31.6 - - + -
34C ALA 3.8 1.0 + - - -
35C TYR* 1.3 72.0 - - - +
37C ALA* 1.3 57.8 + - - +
38C PRO* 3.8 18.2 - - - -
39C LYS* 4.0 10.1 - - + -
40C LYS* 2.9 22.9 + - - -
41C GLU 2.9 22.6 + - - +
43C VAL* 4.5 2.5 - - + -
----------------------------------------------------------
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