Contacts of the strand formed by residues 28 - 37 (chain C) in PDB entry 1VF5
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 28 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C HIS 3.2 3.9 + - - +
27C LEU* 1.3 77.3 - - - +
29C ALA* 1.3 61.3 + - - +
30C LYS* 5.6 3.6 - - - +
159C GLN* 4.0 2.0 + - - +
236C ASN* 2.9 30.1 - - - +
238C GLY 2.9 25.6 - - - +
239C GLY* 2.7 3.8 - - - -
240C PHE* 2.7 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 4.0 2.1 + - - +
28C ALA* 1.3 73.9 - - - +
30C LYS* 1.3 77.9 + - - +
240C PHE 3.3 7.6 - - - +
241C GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 5.6 2.8 - - - +
29C ALA* 1.3 85.3 + - - +
31C PRO* 1.3 82.3 - - + +
53C PRO 5.6 0.9 - - - +
54C TYR* 4.6 22.1 - - + -
155C ARG* 3.6 24.7 - - + +
237C VAL* 3.6 24.3 + - - +
238C GLY* 4.4 2.7 - - - -
239C GLY 3.7 18.6 - - - +
240C PHE 2.9 4.8 + - - -
241C GLY* 3.1 17.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS* 1.3 105.0 - - + +
32C ALA* 1.3 63.9 + - - +
53C PRO* 3.8 24.9 - - + +
155C ARG* 2.8 31.3 + - - +
241C GLY* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 1.3 80.9 - - - +
33C GLU* 1.3 62.4 + - - +
51C LYS 3.6 10.3 - - - -
53C PRO* 4.7 1.7 - - - +
151C LEU* 4.5 3.1 - - + -
153C ALA* 3.9 12.1 - - + -
241C GLY 3.0 34.8 - - - +
242C GLN 3.6 10.8 + - - +
243C ASP* 3.3 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 1.3 75.6 - - - +
34C VAL* 1.3 75.1 + - - +
35C GLU* 2.9 35.4 - - - +
49C VAL 4.1 0.4 - - - -
50C VAL* 3.2 1.4 - - - -
51C LYS* 3.0 55.3 + - + +
151C LEU* 3.0 11.9 - - - +
243C ASP* 3.8 10.8 - - - +
1F MET* 3.3 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU* 1.3 79.5 - - - +
35C GLU* 1.3 62.9 + - - +
36C VAL* 4.0 12.1 + - + -
48C ALA* 5.6 0.9 - - + -
49C VAL 3.4 3.6 - - - +
50C VAL* 4.5 8.5 - - + -
76C LEU* 4.2 14.1 - - + -
149C ILE* 4.0 15.7 - - + -
150C HIS 4.9 0.9 - - - -
151C LEU* 3.2 34.5 - - + +
243C ASP* 3.3 24.4 + - - +
245C THR* 3.8 26.7 - - + +
1F MET* 3.7 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU* 2.9 28.7 - - - +
34C VAL* 1.3 74.1 - - - +
36C VAL* 1.3 60.3 + - - +
47C LYS* 3.9 2.9 - - - +
48C ALA* 3.3 5.9 - - - -
49C VAL* 2.8 46.2 + - + +
51C LYS* 3.1 25.1 + - - -
1F MET* 3.6 17.1 - - + +
4F GLU* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.0 16.1 + - + -
35C GLU* 1.3 82.1 - - - +
37C PRO* 1.3 84.0 - - + +
38C GLN* 3.5 1.7 + - - -
46C PHE* 4.8 4.5 - - + -
47C LYS 4.3 0.7 - - - +
48C ALA* 3.8 22.2 - - + -
78C LEU* 6.2 1.3 - - + -
149C ILE* 3.9 31.9 - - + -
245C THR* 4.3 11.4 + - + +
246C GLU 4.3 8.8 - - - +
247C ILE* 4.0 12.6 - - + -
1F MET* 5.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU 4.8 0.2 - - - +
36C VAL* 1.3 91.5 - - + +
38C GLN* 1.3 67.7 + - - +
39C SER 3.0 11.3 + - - +
40C VAL* 3.2 31.0 - - + -
46C PHE* 3.9 9.2 - - + -
47C LYS* 3.6 17.5 - - + +
247C ILE* 3.1 20.5 - - + +
----------------------------------------------------------
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