Contacts of the strand formed by residues 59 - 68 (chain D) in PDB entry 2VCK
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 59 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D TRP 3.9 0.2 - - - +
48D ASP* 3.6 4.3 - - - -
49D GLY 2.9 28.5 + - - +
50D GLY* 3.6 24.7 - - - +
57D GLY 4.4 0.7 - - - +
58D ASP* 1.3 80.0 + - - +
60D LYS* 1.3 64.5 + - - +
79D ILE* 5.3 4.5 - - + -
80D VAL 3.4 4.7 - - - +
81D ASP* 3.8 14.6 - - + +
215D LYS* 4.4 11.9 - - + -
216D PHE* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS* 6.4 0.2 - - - +
47D TRP 3.4 4.3 - - - +
48D ASP* 3.2 34.7 + - - +
57D GLY 2.8 28.8 + - - +
58D ASP* 4.8 3.1 - - - +
59D ALA* 1.3 77.8 - - - +
61D LEU* 1.3 61.0 + - - +
62D THR* 5.7 2.0 - - - +
78D HIS 3.6 1.6 - - - +
79D ILE* 3.2 5.9 - - - +
80D VAL* 2.8 52.1 + - + +
216D PHE* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ALA* 4.0 14.1 - - + -
46D LYS* 3.2 7.6 + - - -
47D TRP* 3.0 68.0 + - + +
60D LYS* 1.3 74.5 - - - +
62D THR* 1.3 83.5 + - - +
63D ALA* 4.0 3.1 - - + -
77D ALA* 4.4 0.2 - - + -
78D HIS 3.4 4.9 - - - +
79D ILE* 3.5 31.2 - - + +
212D MSE 4.2 2.0 - - + -
216D PHE* 3.9 21.4 - - + -
224D PHE* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 5.3 0.2 - - + -
45D ALA 3.5 2.9 - - - -
46D LYS* 2.9 36.8 + - + +
60D LYS* 5.7 2.1 - - - +
61D LEU* 1.3 76.9 - - - +
63D ALA* 1.3 62.0 + - - +
64D ASN* 3.7 30.5 + - - +
76D GLU* 3.7 1.7 - - - +
77D ALA* 3.5 2.1 - - - -
78D HIS* 2.9 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 3.6 1.4 - - - -
44D TRP* 2.8 42.1 + - + -
45D ALA 2.8 25.4 + - - +
61D LEU* 4.0 17.3 - - + -
62D THR* 1.3 74.8 - - - +
64D ASN* 1.3 55.7 + - - +
76D GLU 3.4 5.2 - - - -
228D PHE* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE* 3.7 31.3 - - + +
42D GLU 3.6 3.6 - - - +
43D VAL* 3.7 23.4 - - - +
62D THR* 3.7 26.4 - - - +
63D ALA* 1.3 76.4 - - - +
65D ILE* 1.3 64.4 + - - +
66D ARG* 4.0 1.9 - - + +
74D ALA 3.9 0.9 - - - +
75D ARG* 3.4 1.2 - - - -
76D GLU* 2.8 63.1 + - + +
228D PHE* 3.4 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE* 3.6 1.7 - - - -
41D SER* 2.7 41.0 + - - +
42D GLU* 2.8 51.1 + - + +
44D TRP* 4.1 17.0 - - + -
63D ALA 4.3 0.2 + - - -
64D ASN* 1.3 72.7 - - - +
66D ARG* 1.3 63.3 + - - +
67D THR* 4.5 4.3 - - + -
73D LYS* 4.4 20.4 - - + -
74D ALA 3.8 2.9 - - - +
75D ARG* 4.7 4.5 - - + +
228D PHE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 5.7 1.2 - - - +
32D PHE* 3.3 41.2 - - - +
38D LEU* 3.0 31.1 + - + -
39D GLU* 3.2 20.6 + - - +
40D ILE* 3.7 33.6 - - + +
64D ASN* 4.5 3.7 - - + +
65D ILE* 1.3 74.8 - - - +
67D THR* 1.3 65.1 + - - +
73D LYS* 3.2 7.8 - - - +
74D ALA* 2.8 47.0 + - + +
76D GLU* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN 3.1 13.2 - - - +
38D LEU* 3.6 7.1 - - - -
39D GLU* 3.1 15.9 + - - +
41D SER* 3.1 29.4 + - - +
65D ILE* 4.5 9.2 - - + -
66D ARG* 1.3 79.8 - - - +
68D GLY* 1.3 59.6 + - - +
71D PHE 5.2 1.6 - - - -
72D LEU 3.8 18.6 - - - +
73D LYS* 4.8 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN* 3.5 19.3 - - - -
38D LEU* 4.1 3.3 - - - +
67D THR* 1.3 79.2 - - - +
69D GLU* 1.3 69.5 + - - -
70D HIS 3.3 0.3 + - - -
71D PHE* 3.0 24.9 + - - +
94D LYS* 4.8 2.6 - - - -
----------------------------------------------------------
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