Contacts of the helix formed by residues 82 - 91 (chain A) in PDB entry 3K4H
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 ASP 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 3.5 - - - +
77A TYR* 2.6 44.6 + - - +
79A ARG* 3.6 30.4 + - + +
80A GLU 3.3 2.7 - - - -
81A ASN* 1.3 75.5 - - - +
83A ARG* 1.3 66.5 + - - +
84A ILE* 3.3 24.9 + - - +
85A ILE* 3.3 24.2 + - + +
86A GLN* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 2.7 51.1 + - - -
55A GLU* 4.2 10.5 - - - +
58A PHE* 3.2 55.1 - - + +
59A ASN* 5.4 0.6 + - - -
81A ASN 3.0 12.5 + - - +
82A ASP* 1.3 73.6 + - - +
84A ILE* 1.3 65.2 + - + +
86A GLN* 2.9 11.5 + - - +
87A TYR* 2.8 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.8 1.8 - - + -
57A ILE* 4.1 11.2 - - + +
58A PHE* 3.7 42.2 - - + +
61A VAL* 3.8 38.4 - - + -
75A LEU* 4.0 16.6 - - + -
77A TYR* 3.5 11.0 - - - +
79A ARG* 5.7 0.4 - - - +
82A ASP* 3.1 22.6 - - - +
83A ARG* 1.3 77.6 - - + +
85A ILE* 1.3 58.4 + - - +
87A TYR* 3.2 4.1 + - - +
88A LEU* 3.0 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.5 28.5 - - + -
78A SER* 5.7 1.6 - - - +
79A ARG 4.9 7.0 - - - +
82A ASP* 3.3 24.3 + - + +
83A ARG 3.2 0.4 - - - -
84A ILE* 1.3 72.7 - - - +
86A GLN* 1.3 60.1 - - - +
87A TYR 3.1 1.3 - - - -
88A LEU* 4.4 4.9 - - - +
89A HIS* 2.8 30.8 + - + +
95A PHE* 3.9 22.0 - - + -
97A LEU* 4.2 24.0 - - + -
101A PRO* 5.6 2.5 - - + -
104A ARG* 4.7 11.9 - - - +
108A ILE* 4.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP 3.2 9.6 + - - +
83A ARG* 2.9 17.3 + - - +
85A ILE* 1.3 73.6 - - - +
87A TYR* 1.3 62.5 + - - +
89A HIS* 4.0 3.2 - - - +
90A GLU* 3.1 50.6 + - - +
104A ARG* 3.4 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.9 22.9 - + + -
61A VAL* 4.3 7.6 - - + -
62A VAL* 3.8 29.2 + - + -
65A VAL* 3.6 38.0 - - + +
66A GLN* 4.1 19.5 + - - +
83A ARG 2.8 11.0 + - - +
84A ILE* 3.3 8.3 - - - +
86A GLN* 1.3 79.5 - - - +
88A LEU* 1.3 70.9 + - + +
90A GLU* 3.7 3.2 - - + +
91A GLN* 3.0 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.8 4.3 - - + -
65A VAL* 3.8 20.4 - - + -
73A ILE* 3.7 37.7 - - + -
75A LEU* 4.7 5.4 - - + -
84A ILE* 3.0 32.2 + - + +
85A ILE* 4.0 2.7 - - - +
87A TYR* 1.3 85.9 - - + +
89A HIS* 1.3 62.4 + - - +
91A GLN* 3.4 0.8 + - - +
92A ASN* 3.2 3.6 + - - -
93A PHE* 2.9 41.8 + - + +
95A PHE* 3.6 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 2.8 19.5 + - + +
86A GLN* 4.0 3.6 - - - +
88A LEU* 1.3 78.2 - - - +
90A GLU* 1.3 77.7 + - + +
92A ASN* 3.2 16.2 + - - +
95A PHE* 4.3 13.2 - - + -
104A ARG* 3.2 42.3 + - - +
107A GLU* 3.7 28.5 + - + +
108A ILE* 6.1 2.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
86A GLN* 3.1 40.0 + - - +
87A TYR* 3.7 4.5 - - - +
89A HIS* 1.3 87.2 + - + +
91A GLN* 1.3 72.5 + - - +
92A ASN* 3.0 9.2 + - - +
104A ARG* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.7 12.1 - - + -
87A TYR* 3.0 58.7 + - + +
88A LEU 3.4 2.7 + - - +
90A GLU* 1.3 91.3 + - - +
92A ASN* 1.3 70.4 + - - +
93A PHE* 3.2 6.1 + - + +
----------------------------------------------------------
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