Contacts of the helix formed by residues 82 - 92 (chain A) in PDB entry 3KVT
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 GLY 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.3 22.0 - - - -
80A VAL 3.9 0.4 + - - -
81A CYS* 1.3 71.4 - - - +
83A PRO* 1.3 65.1 - - - +
85A PHE* 3.2 4.5 + - - +
86A GLU* 2.8 39.5 + - - +
106A THR* 4.5 13.4 + - - -
107A TYR* 6.1 0.2 - - - -
110A HIS* 5.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS* 3.5 15.9 - - + -
82A GLY* 1.3 90.4 - - - +
84A LEU* 1.3 61.0 + - - +
86A GLU* 3.4 11.8 + - + +
87A GLU* 3.0 29.8 + - - +
110A HIS* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 4.0 22.2 - - + +
61A VAL* 3.7 28.5 - - + -
80A VAL* 4.3 17.9 - - + -
81A CYS* 3.3 23.5 + - - +
83A PRO* 1.3 77.8 - - - +
85A PHE* 1.3 65.1 + - - +
87A GLU* 3.2 23.1 + - + +
88A GLU* 3.3 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.4 27.1 - - + -
64A GLN* 3.9 14.8 - - + -
65A ILE* 3.8 15.0 - - + -
74A LEU* 4.0 5.8 - - + -
75A HIS 3.6 18.6 - - - -
76A TYR* 3.6 33.7 - + + -
77A PRO* 3.4 31.9 - - + -
80A VAL* 4.5 1.1 - - + -
81A CYS 3.3 8.7 + - - +
82A GLY* 3.2 10.6 + - - +
84A LEU* 1.3 84.8 - - - +
86A GLU* 1.3 56.3 + - - +
88A GLU* 2.9 9.3 + - - +
89A LEU* 2.8 58.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
76A TYR* 2.7 38.0 + - + +
82A GLY* 2.8 25.7 + - - +
83A PRO* 3.8 11.3 - - + +
85A PHE* 1.3 73.9 - - - +
87A GLU* 1.3 65.2 + - - +
89A LEU* 3.1 13.2 + - + +
90A GLU* 2.9 35.1 + - - +
96A SER* 4.3 8.7 - - - +
107A TYR* 3.6 19.9 - - - +
110A HIS* 5.5 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 3.8 13.5 + - - +
83A PRO* 3.0 18.4 + - - +
84A LEU* 3.4 17.5 - - + +
85A PHE 3.2 0.2 - - - -
86A GLU* 1.3 75.9 - - - +
88A GLU* 1.3 68.3 + - - +
90A GLU* 3.4 12.9 + - - +
91A PHE* 3.1 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.9 53.9 + - - +
58A HIS* 3.7 17.5 + - - +
61A VAL* 3.7 30.5 - - + -
65A ILE* 4.2 7.4 - - + -
84A LEU* 3.5 20.5 - - + +
85A PHE 2.9 8.6 + - - +
87A GLU* 1.3 79.6 - - - +
89A LEU* 1.3 64.5 + - - +
91A PHE* 3.3 0.7 + - - +
92A TRP* 2.9 40.1 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
65A ILE* 3.6 21.8 - - + -
74A LEU* 4.0 15.0 - - + -
76A TYR* 3.9 8.1 - - + +
85A PHE* 2.8 47.4 + - + +
86A GLU* 3.1 13.2 + - - +
88A GLU* 1.3 76.7 - - - +
90A GLU* 1.3 57.7 + - + +
92A TRP 3.5 0.7 + - - -
93A GLY 3.1 6.9 + - - -
94A LEU* 2.9 56.9 + - + +
96A SER* 3.8 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.2 0.5 + - - -
86A GLU* 2.9 25.8 + - + +
87A GLU* 3.7 10.0 - - - +
88A GLU 3.2 0.2 - - - -
89A LEU* 1.3 74.8 - - + +
91A PHE* 1.3 65.2 + - - +
93A GLY* 3.2 12.2 + - - -
94A LEU 4.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.9 70.8 + - - +
55A PHE* 3.9 13.9 - + - -
56A ASP 6.0 0.2 - - - -
57A ARG* 3.3 64.8 - - + +
87A GLU 3.1 7.2 + - - +
88A GLU 3.3 5.1 + - - +
90A GLU* 1.3 76.7 - - - +
92A TRP* 1.3 92.1 + + - +
93A GLY* 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.3 2.5 - - + -
34A THR* 3.6 6.1 - - - -
35A ARG* 3.2 34.9 + - + +
36A LEU* 3.8 34.2 + - + -
55A PHE* 3.5 42.2 - + + -
57A ARG* 3.8 14.7 - - + +
58A HIS 5.9 0.4 + - - -
62A PHE* 3.4 34.1 - + - +
65A ILE* 3.8 21.9 - - + +
69A TYR* 4.4 3.8 + - - +
88A GLU* 2.9 43.5 + - + +
89A LEU 4.2 0.4 - - - +
91A PHE* 1.3 102.5 - + - +
93A GLY* 1.3 60.1 + - - +
94A LEU* 3.4 21.1 + - + +
----------------------------------------------------------
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