Contacts of the strand formed by residues 102 - 107 (chain B) in PDB entry 4JDA
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 ILE 102 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.8 3.1 - - - +
88B ARG* 3.0 27.2 + - + -
89B VAL* 3.1 33.5 + - + +
100B GLY 3.5 1.2 + - - -
101B THR* 1.3 76.0 - - - +
103B ARG* 1.3 62.1 + - - +
117B VAL* 5.5 5.8 - - + -
118B GLU 3.5 8.1 - - - +
119B ILE* 3.9 15.9 - - + -
135B LEU* 5.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.0 74.6 + - + +
75B PRO* 4.4 9.2 - - - +
79B LYS* 3.9 22.8 - - - +
85B CYS* 3.4 24.7 - - - -
86B THR 3.5 7.4 - - - +
87B ILE* 4.3 4.5 - - + +
88B ARG* 5.0 2.7 - - - -
102B ILE* 1.3 74.7 - - - +
104B GLU* 1.3 61.4 + - - +
105B VAL* 3.8 22.3 - - + +
116B SER 3.9 0.2 - - - +
117B VAL* 3.4 6.4 - - - +
118B GLU* 3.0 50.6 + - + +
130B LEU* 5.3 2.0 - - - +
132B PHE* 4.1 19.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 4.2 0.2 - - - +
85B CYS* 3.5 2.6 - - - -
86B THR* 2.8 37.0 + - - -
88B ARG* 2.7 52.3 + - + +
103B ARG* 1.3 73.2 - - - +
105B VAL* 1.3 63.4 + - - +
106B SER* 4.0 0.7 + - - -
115B THR* 3.2 30.1 + - - +
116B SER 3.3 8.3 - - - +
117B VAL* 4.5 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 4.6 3.8 - - + -
82B ILE* 4.0 33.4 - - + -
84B SER 3.7 4.7 - - - -
85B CYS* 4.4 1.8 - - - +
103B ARG* 3.8 34.1 - - + +
104B GLU* 1.3 75.1 - - - +
106B SER* 1.3 62.3 + - - +
107B VAL* 5.2 3.4 - - + -
115B THR* 2.9 24.3 + - - -
116B SER* 2.7 36.9 + - - +
118B GLU* 5.9 0.4 - - + -
301B A9S 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 3.8 0.7 - - - -
83B LYS* 2.9 31.4 + - - +
84B SER* 2.7 40.4 + - - +
104B GLU 4.0 1.1 + - - -
105B VAL* 1.3 75.1 - - - +
107B VAL* 1.3 62.6 + - - +
114B SER 3.4 7.0 - - - -
115B THR* 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE 3.4 13.5 - - - +
82B ILE* 4.6 2.7 - - + +
83B LYS* 4.3 4.0 - - - +
105B VAL* 4.8 7.0 - - + +
106B SER* 1.3 77.3 - - - +
108B VAL* 1.3 76.2 + - - +
109B SER* 3.4 2.8 + - - -
111B LEU* 4.2 12.8 - - + -
113B ALA* 3.4 27.2 - - + +
114B SER* 2.8 27.4 + - - +
115B THR* 3.8 10.5 - - - +
116B SER* 4.9 2.7 - - - +
301B A9S 3.8 32.3 - - + +
----------------------------------------------------------
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