Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 4D0N
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 VAL 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 3.2 3.5 + - - +
8A LEU* 3.3 29.0 - - + +
9A VAL 3.2 23.2 + - - +
55A LEU* 4.6 4.3 - - + -
77A THR* 3.2 5.4 - - - +
78A ASP* 1.3 81.7 - - - +
80A ILE* 1.3 74.5 + - - +
81A LEU* 5.2 0.2 - - + -
110A VAL* 3.8 1.1 - - - -
111A PRO 3.6 14.1 - - - +
113A ILE* 4.1 5.4 - - + -
174A ALA* 3.6 40.4 - - + +
177A ALA* 4.1 10.5 - - + -
178A ALA* 4.1 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.4 18.2 - - + +
11A VAL* 4.0 15.3 - - + -
74A TYR* 4.3 12.3 - - + -
77A THR* 3.9 20.6 - - + -
79A VAL* 1.3 78.3 - - - +
81A LEU* 1.3 77.2 + - - +
82A MET* 4.1 7.4 - - + +
103A VAL* 3.8 30.7 - - + -
107A CYS* 4.2 13.5 - - - -
110A VAL* 4.1 11.2 - - + -
111A PRO 3.1 10.5 + - - +
112A ILE* 3.4 6.4 - - + -
113A ILE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 19.1 - - + -
9A VAL 3.0 6.5 + - - +
10A ILE* 3.3 27.3 - - + +
11A VAL* 2.9 30.3 + - - +
21A LEU* 4.5 2.5 - - + -
22A LEU* 5.2 0.2 - - + -
79A VAL 4.2 0.4 - - - -
80A ILE* 1.3 71.5 - - - +
82A MET* 1.3 61.0 + - - +
83A CYS* 4.0 0.9 - - - -
113A ILE* 3.7 25.6 - - + -
115A VAL* 4.3 7.4 - - + -
170A VAL* 3.9 21.1 - - + -
171A PHE* 3.8 35.0 - - + -
174A ALA* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 16.4 - - + +
80A ILE* 3.8 1.7 + - + -
81A LEU* 1.3 70.7 - - - +
83A CYS* 1.3 60.3 + - - +
95A ILE* 3.6 38.4 - - + -
99A TRP* 3.8 31.6 - - + +
100A THR* 3.8 17.0 - - - +
103A VAL* 3.9 15.5 - - + -
112A ILE* 3.7 37.7 - - + -
113A ILE 2.8 9.6 + - - +
114A LEU* 3.4 10.7 - - + +
115A VAL* 2.9 24.0 + - - +
151A ILE* 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.3 38.6 - - - -
11A VAL 2.9 15.0 + - - +
12A GLY* 3.3 20.3 - - - -
13A ASP 4.1 2.1 + - - -
16A CYS* 3.6 19.9 - - - -
18A LYS* 4.6 0.7 - - + -
21A LEU* 4.5 0.4 - - - -
81A LEU 4.4 1.1 - - - -
82A MET* 1.3 75.8 - - - +
84A PHE* 1.3 58.9 + - - +
91A SER 4.8 0.5 - - - +
95A ILE* 3.6 10.2 - - - +
99A TRP* 5.3 0.2 - - - -
115A VAL* 3.3 26.0 - - - +
117A ASN* 3.6 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 4.0 9.0 - - - -
83A CYS* 1.3 74.8 - - - +
85A SER* 1.3 70.4 + - - +
86A ILE* 4.2 7.0 - - + -
91A SER* 3.3 29.4 - - - +
92A LEU* 3.6 35.0 - - + +
95A ILE* 4.0 2.2 - - + -
114A LEU* 3.9 19.5 - - + -
115A VAL 3.0 13.0 + - - +
116A GLY* 3.7 17.9 - - - -
117A ASN* 2.9 28.9 + - - +
139A VAL* 3.8 29.6 - - + -
144A GLY* 4.5 2.0 - - - -
156A TYR* 3.5 37.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 5.0 1.1 - - - -
16A CYS* 4.0 24.7 - - - +
84A PHE* 1.3 80.7 - - - +
86A ILE* 1.3 57.5 + - - +
87A ASP* 2.2 32.2 + - - -
88A SER* 2.8 38.7 + - - +
91A SER* 2.8 13.8 + - - -
117A ASN 3.7 3.8 - - - -
118A LYS* 3.4 15.6 - - - +
139A VAL* 4.1 0.2 - - - +
----------------------------------------------------------
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