Contacts of the strand formed by residues 100 - 107 (chain H) in PDB entry 4OZF
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 ALA 100 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 4.3 13.2 - - + -
44H GLN 3.8 19.3 - - - +
45H SER* 4.0 12.3 - - - +
98H ASP 3.5 2.0 + - - -
99H SER* 1.4 74.4 - - - +
101H VAL* 1.3 66.8 + - - +
102H TYR* 3.5 18.5 - - + -
122H THR 3.5 2.1 - - - +
123H ARG* 4.7 1.8 - - - -
124H LEU 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G SER* 5.3 15.5 - - - +
48G GLN* 6.0 3.6 - - - -
43H ARG* 3.3 1.9 - - - -
44H GLN* 2.9 46.3 + - - +
100H ALA* 1.3 71.5 - - - +
102H TYR* 1.3 62.5 + - - +
103H LEU* 3.5 24.9 + - + +
120H PRO 5.0 2.5 - - - +
121H GLY* 4.0 16.8 - - - -
122H THR 3.3 5.8 - - - +
123H ARG* 3.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 2.8 27.0 + - - -
21H LEU* 3.6 30.5 - - + -
41H TRP* 4.7 6.3 - + + -
42H TYR 3.5 2.5 - - - +
43H ARG* 3.1 43.8 + - + -
53H LEU* 3.7 23.3 - - + -
76H PHE* 3.4 19.8 - + - -
89H LEU* 4.3 3.4 - - + -
91H ILE* 4.0 8.6 - - + +
98H ASP 2.6 30.8 + - - -
100H ALA* 3.5 19.3 - - + -
101H VAL* 1.3 69.9 - - - +
103H LEU* 1.3 55.6 + - - +
122H THR* 2.8 30.0 + - - +
124H LEU* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLN* 4.6 0.2 - - - +
48G GLN 4.9 0.4 - - - +
49G GLY* 3.7 28.7 - - - +
50G PRO* 3.9 14.4 - - + -
6H GLN* 3.7 2.0 - - - +
41H TRP* 3.6 4.9 - - - -
42H TYR* 2.7 46.4 + - + +
44H GLN* 3.6 31.4 - - + +
50H LEU* 3.9 22.9 - - + -
101H VAL* 3.5 14.3 + - + +
102H TYR* 1.3 72.7 - - - +
104H CYS* 1.3 58.9 + - - +
118H PHE* 4.1 11.0 - - + -
119H GLY 3.7 12.6 - - - +
121H GLY* 3.8 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.2 2.2 - - + +
6H GLN* 3.0 24.1 + - + +
23H CYS* 2.0 53.4 - - + -
39H LEU* 3.5 21.5 - - - -
40H TYR 3.3 5.6 - - - -
41H TRP* 4.0 7.2 - - + -
103H LEU* 1.3 73.4 - - - +
105H ALA* 1.3 65.8 + - - +
118H PHE* 3.3 5.8 - - - +
119H GLY 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.8 1.8 - - - -
39H LEU* 3.4 6.6 - - - +
40H TYR* 2.7 36.7 + - + +
42H TYR* 4.1 13.2 - - + -
104H CYS* 1.3 76.1 - - - +
106H SER* 1.3 61.7 + - - +
116H GLN* 4.2 12.8 - - + -
117H TYR 3.2 13.7 - - - +
118H PHE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 3.4 19.9 - - - +
25H PRO* 3.7 23.3 - - - -
26H ILE* 3.4 9.0 + - - +
29H HIS* 3.2 21.9 + - - -
38H ALA 3.3 13.2 - - - -
40H TYR* 4.2 1.8 - - - -
105H ALA* 1.3 77.9 - - - +
107H SER* 1.3 61.4 + - - +
115H THR 3.5 1.9 - - - +
116H GLN* 4.3 1.3 - - - -
117H TYR* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H HIS* 3.1 25.3 - - - +
38H ALA* 3.1 13.5 + - - +
40H TYR* 2.9 32.3 + - - -
106H SER* 1.3 71.5 - - - +
108H PHE* 1.4 64.4 + - - +
109H ARG 2.9 13.2 + - - -
114H ASP* 3.7 17.5 - - - -
115H THR 3.2 23.6 - - - -
116H GLN* 4.1 1.6 - - - -
----------------------------------------------------------
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