Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 3V4V
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 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.0 33.8 + - - +
41A ALA* 3.9 6.3 - - + +
43A TRP* 3.7 14.1 - - + +
53A GLY* 1.3 75.8 - - - -
55A ILE* 1.3 66.6 + - - +
56A TYR* 4.1 6.0 - - + -
70A GLN* 3.6 39.0 - - + +
71A LEU 3.9 5.8 - - - +
94A LEU* 4.0 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 5.3 8.1 - - + -
36A VAL 3.2 12.8 - - - +
37A GLY* 4.6 1.1 - - - -
54A ALA* 1.3 77.2 - - - +
56A TYR* 1.3 68.4 + - - +
70A GLN* 3.9 0.5 - - - +
71A LEU* 2.9 53.2 + - + +
73A LEU* 4.1 14.1 - - + +
94A LEU* 4.7 5.5 - - + +
95A GLY* 3.7 16.2 - - - +
98A LEU* 4.3 15.0 - - + -
108A ILE* 5.7 2.5 - - + -
110A THR* 3.6 42.8 - - + +
135A VAL* 5.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 3.4 31.4 - - + +
17A THR* 5.0 0.3 - - - +
19A PHE* 3.9 26.7 - + + -
34A LEU 4.6 0.2 - - - -
35A LEU* 3.5 8.7 - - - +
36A VAL* 2.7 32.2 + - + +
38A ALA* 4.1 19.3 - - + -
41A ALA* 4.1 13.3 - - + +
42A ASN 4.9 0.3 + - - -
54A ALA 4.1 7.0 - - - -
55A ILE* 1.3 84.6 - - - +
57A ARG* 1.3 63.6 + - - +
58A CYS* 5.2 0.2 - - - -
68A CYS* 4.3 16.4 - - + -
69A GLU 3.4 12.6 - - - +
70A GLN* 3.2 54.4 + - + -
71A LEU* 3.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.7 29.5 - - + -
34A LEU 3.6 4.9 - - - -
35A LEU* 3.6 17.7 - - + -
56A TYR* 1.3 77.7 - - - +
58A CYS* 1.3 62.5 + - - +
59A ARG 4.3 0.3 + - - -
67A THR 4.3 0.2 - - - +
68A CYS* 3.6 1.6 - - - -
69A GLU* 3.0 65.3 + - + +
71A LEU* 3.5 23.8 - - + +
138A ASP 4.2 5.3 + - - -
139A LEU* 3.5 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.6 26.5 - - + -
19A PHE* 4.4 8.7 - - - -
33A TRP* 3.6 4.2 - - - -
34A LEU* 2.9 44.1 + - + +
36A VAL* 4.4 5.4 - - - -
56A TYR* 5.1 0.2 - - - -
57A ARG* 1.3 77.0 - - - +
59A ARG* 1.3 66.4 + - - +
60A ILE* 3.4 4.2 + - - +
67A THR 3.9 5.4 - - - +
68A CYS* 2.0 49.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 2.8 21.5 + - - -
30A ALA 5.6 0.6 + - - -
31A ASN* 2.7 40.9 + - - +
32A ARG 3.8 8.4 - - - +
33A TRP* 3.4 43.5 - - + -
57A ARG 4.3 0.2 + - - -
58A CYS* 1.3 72.6 - - - +
60A ILE* 1.3 68.3 + - - +
62A LYS* 3.4 47.5 - - - +
63A ASN* 3.1 28.8 + - - +
67A THR 4.4 0.6 + - - -
----------------------------------------------------------
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