Contacts of the helix formed by residues 80 - 90 (chain A) in PDB entry 1VCN
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 LEU 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 4.4 4.5 - - - -
68A GLU* 3.8 33.7 + - + +
70A PHE* 4.2 10.5 - - - -
78A THR 3.6 1.2 + - - -
79A ASP* 1.3 79.6 - - - +
81A ASP* 1.3 82.8 + - - +
82A ILE 3.1 0.7 - - - -
83A GLY* 3.0 13.6 + - - -
84A HIS* 3.4 15.8 + - + +
87A ARG* 4.7 0.2 + - - -
314A ASP* 3.9 44.9 - - + +
317A LEU* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.7 23.1 - - - -
49A LYS* 2.8 40.8 + - + +
79A ASP* 3.0 12.6 + - - +
80A LEU* 1.3 85.5 - - - +
82A ILE* 1.3 63.6 + - - +
84A HIS* 2.9 19.8 + - - +
85A TYR* 2.9 43.3 + - + +
151A GLU* 4.1 3.2 - - - +
610A SO4 3.8 5.2 + - - -
620A SO4 4.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 3.9 16.8 - - + -
70A PHE* 3.8 8.1 - - + -
72A THR* 3.8 28.3 - - + -
78A THR* 3.1 31.4 - - + +
79A ASP* 3.4 5.6 - - + +
80A LEU 3.1 0.2 - - - -
81A ASP* 1.3 77.5 - - - +
83A GLY* 1.3 56.5 + - - +
85A TYR* 3.1 16.3 + - + +
86A GLU* 2.9 27.8 + - + +
93A LEU* 4.1 17.0 - - + -
94A SER 5.4 0.7 - - - +
97A ASN* 3.4 31.9 - - + +
98A ASN* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU* 5.3 0.2 - - - -
70A PHE* 3.7 36.7 - - - -
80A LEU 3.0 9.4 + - - -
82A ILE* 1.3 80.9 - - - +
84A HIS* 1.4 54.6 + - - +
86A GLU* 3.5 1.8 + - - +
87A ARG* 3.0 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 4.7 5.6 - - - +
29A ILE* 3.6 30.2 - - + +
32A SER* 3.4 16.4 - - - +
80A LEU* 3.4 12.2 + - + +
81A ASP* 2.9 35.7 + - - +
83A GLY* 1.4 72.4 - - - +
85A TYR* 1.3 62.3 + - + +
87A ARG* 3.3 16.1 + - - +
88A PHE* 2.9 39.9 + - + -
255A LEU* 5.3 6.1 - - + +
317A LEU* 3.4 34.9 - - + +
321A GLU* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.9 4.5 - - - -
31A THR* 3.7 25.4 - - + -
32A SER* 3.4 20.6 - - - -
47A ALA* 3.4 33.9 - - + -
48A ILE 3.9 0.9 - - - -
49A LYS* 3.5 39.6 - - + +
81A ASP* 2.9 25.1 + - + -
82A ILE* 3.1 13.0 + - + +
84A HIS* 1.3 78.4 - - - +
86A GLU* 1.3 58.6 + - - +
89A LEU* 2.8 40.5 + - + +
93A LEU* 3.6 17.7 - - + -
151A GLU* 2.7 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.4 16.3 - - + -
72A THR* 4.1 3.1 - - - +
82A ILE 2.9 18.3 + - - +
83A GLY* 3.8 6.7 - - - +
84A HIS 3.3 0.2 - - - -
85A TYR* 1.3 77.4 - - - +
87A ARG* 1.3 54.9 + - + +
90A ASP* 2.7 35.2 + - - -
91A MET 3.1 24.4 + - - +
93A LEU* 3.1 35.3 + - + +
468A ARG* 3.0 34.7 + - - -
525A PHE 3.9 3.4 - - - +
528A ARG* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU* 5.1 0.4 + - - -
70A PHE* 4.5 3.6 - - - -
80A LEU 4.7 0.4 + - - -
83A GLY* 3.0 37.9 + - - +
84A HIS* 3.5 29.8 + - - +
86A GLU* 1.3 78.0 - - + +
88A PHE* 1.3 69.1 + - + +
90A ASP* 3.9 6.2 + - - +
256A TYR* 5.6 0.4 - - + -
287A TRP* 4.5 1.4 - - - -
317A LEU* 3.7 24.2 - - - +
318A SER* 3.1 29.5 + - - +
321A GLU* 3.5 23.6 + - - +
325A HIS* 3.7 28.7 - - + -
524A GLU 5.2 2.4 + - - -
525A PHE 5.5 1.7 + - - +
527A SER 3.5 17.5 + - - +
528A ARG* 4.1 9.1 - - + +
529A PRO* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.3 13.9 - - + -
32A SER* 3.4 43.3 - - - +
33A SER* 3.9 20.6 - - - -
36A ALA* 3.9 18.0 - - + +
39A ARG* 4.6 5.2 + - - -
84A HIS* 2.9 29.9 + - - +
85A TYR 4.2 1.1 - - - +
87A ARG* 1.3 85.7 - - + +
89A LEU* 1.3 63.2 + - + +
90A ASP* 3.4 1.1 - - - +
255A LEU* 4.0 37.5 - - + -
256A TYR* 4.4 10.3 - + - -
259A PRO* 4.3 11.9 - - + -
287A TRP* 3.7 35.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 4.4 6.1 - - - +
35A GLY* 3.6 36.1 - - - +
36A ALA 3.8 3.6 - - - +
39A ARG* 3.4 37.3 + - + +
45A VAL* 4.3 8.1 - - + +
46A THR* 4.0 13.7 - - - +
47A ALA* 3.9 34.8 - - + +
85A TYR* 2.8 24.3 + - + +
88A PHE* 1.3 78.8 - - + +
90A ASP* 1.3 71.5 + - - +
91A MET* 3.7 19.5 - - + +
93A LEU* 5.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 4.8 11.9 + - - +
86A GLU 2.7 18.3 + - - -
87A ARG 3.9 4.9 + - - +
88A PHE 3.4 3.9 - - - +
89A LEU* 1.3 76.5 - - - +
91A MET* 1.3 56.0 + - - +
528A ARG* 3.2 34.0 + - + +
530A MET* 4.8 18.7 - - + +
531A ARG* 5.4 4.7 - - - +
----------------------------------------------------------
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