Contacts of the strand formed by residues 36 - 44 (chain A) in PDB entry 2VPA
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 ILE 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 1.4 93.4 + - - +
37A ALA* 1.3 66.4 + - - +
38A ARG* 3.9 27.0 + - - +
56A PRO* 4.8 4.0 - - + -
57A LEU* 3.4 22.9 - - - +
58A ALA* 4.1 5.2 - - + +
59A TYR* 3.6 8.7 - - - -
92A VAL* 3.9 15.1 - - - +
93A SER 5.0 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 1.3 75.8 - - - +
38A ARG* 1.3 66.8 + - - +
55A THR 3.8 0.3 - - - +
56A PRO* 3.2 4.0 - - - +
57A LEU* 2.9 37.4 + - + +
59A TYR* 3.5 23.1 - - + -
90A LEU* 3.8 20.9 - - + -
91A GLU 3.3 13.7 - - - +
92A VAL* 3.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.9 22.2 + - - +
37A ALA* 1.3 75.0 - - - +
39A VAL* 1.3 60.7 + - - +
54A ILE* 3.8 27.6 - - + -
55A THR 3.3 2.5 - - - -
56A PRO* 3.8 31.5 - - + +
89A THR 3.9 0.9 - - - +
90A LEU* 3.3 2.8 - - - +
91A GLU* 2.8 54.3 + - + +
93A SER* 5.3 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 1.3 77.9 - - - +
40A ALA* 1.3 62.1 + - - +
41A THR* 4.1 11.2 + - + -
53A PHE* 3.6 1.7 - - - +
54A ILE* 3.4 4.8 - - - -
55A THR* 3.0 33.6 + - - +
57A LEU* 3.9 24.0 - - + -
70A TYR* 3.8 28.5 - - + +
88A ALA* 4.3 5.6 - - + -
89A THR 3.4 9.4 - - - +
90A LEU* 3.9 26.0 - - + -
165A LEU* 5.0 0.9 - - + -
1196A ACT 3.9 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG 4.2 0.4 - - - -
39A VAL* 1.3 72.7 - - - +
41A THR* 1.3 66.1 + - - +
42A LEU* 5.6 1.3 - - + -
52A PRO* 4.6 11.9 - - + -
53A PHE 3.1 15.3 - - - +
54A ILE* 4.6 9.4 - - + -
88A ALA* 3.5 1.9 - - - -
89A THR* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.1 3.0 + - + -
40A ALA* 1.3 79.7 - - - +
42A LEU* 1.3 65.4 + - - +
43A TRP* 3.1 21.6 + - - -
52A PRO* 3.3 2.3 - - - +
53A PHE* 3.0 29.9 + - - +
79A ARG* 4.1 9.9 - - - -
86A HIS* 3.6 16.8 - - + -
87A PRO 4.0 4.5 - - - +
88A ALA* 3.9 11.9 - - + -
1196A ACT 3.5 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 5.6 1.3 - - + -
41A THR* 1.3 78.6 - - - +
43A TRP* 1.3 65.1 + - - +
50A ALA* 4.1 17.3 - - + -
51A PHE* 3.5 4.5 - - - +
52A PRO* 3.8 34.3 - - + -
79A ARG* 3.6 10.2 + - - +
80A ALA* 3.0 38.6 + - + +
81A ASN* 5.1 0.9 - - - +
86A HIS* 6.2 0.2 - - - +
87A PRO* 4.8 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.1 29.2 + - - -
42A LEU* 1.3 80.0 - - - +
44A GLN* 1.3 65.0 + - - +
50A ALA* 3.3 1.0 - - - -
51A PHE* 2.9 41.1 + - + +
53A PHE* 3.5 40.8 - + + -
74A VAL 4.5 3.1 - - - -
75A VAL* 3.7 20.2 - - + -
76A GLY* 3.2 41.7 - - - -
77A ARG 3.8 7.6 - - - +
78A LEU 3.4 20.6 - - - +
79A ARG* 3.4 55.4 - - + -
80A ALA* 3.9 4.0 - - - +
1196A ACT 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 1.3 73.2 - - - +
45A GLY* 1.3 68.6 + - - +
48A GLY* 3.7 25.4 + - - +
49A ALA 3.9 2.9 - - - -
50A ALA* 4.5 0.9 - - - +
51A PHE* 4.1 3.4 - - - -
77A ARG* 4.8 12.6 + - - +
78A LEU* 2.8 44.6 + - + +
79A ARG 4.8 1.9 + - - +
80A ALA* 4.0 15.9 - - + +
----------------------------------------------------------
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