Contacts of the strand formed by residues 38 - 44 (chain F) in PDB entry 4OZH
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 38 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F HIS* 4.4 1.6 - - - +
37F THR* 1.3 79.9 + - - +
39F LEU* 1.3 59.6 + - - +
40F TYR* 3.9 12.8 - - + +
55F TYR* 5.0 0.7 - - + -
56F PHE 3.3 7.4 - - - +
57F GLN* 3.9 6.7 - - - +
80F ARG* 4.1 1.3 + - - -
106F SER* 3.3 8.1 - - - -
107F SER* 3.1 48.8 + - - +
109F ARG* 3.6 18.8 - - - -
110F SER* 3.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F CYS* 4.5 5.4 - - - -
25F PRO* 3.8 24.0 - - + -
38F ALA* 1.3 72.7 - - - +
40F TYR* 1.3 66.7 + - - +
41F TRP* 3.6 32.3 - - + +
55F TYR* 3.2 6.2 - - - +
56F PHE* 2.8 40.0 + - + +
80F ARG* 3.6 23.7 - - - +
85F SER 3.5 24.7 - - - +
87F SER* 3.7 17.7 - - - +
104F CYS* 3.7 15.0 - - - -
105F ALA 3.6 7.9 - - - +
106F SER* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ASN* 2.8 52.1 + - - -
38F ALA* 3.9 13.5 - - + +
39F LEU* 1.3 76.2 - - - +
41F TRP* 1.3 62.7 + - - +
42F TYR* 3.5 25.1 + - + -
52F PHE* 4.2 6.3 - + + -
54F ILE 3.8 3.4 - - - +
55F TYR* 3.5 22.2 - + + -
104F CYS* 3.3 10.0 - - - -
105F ALA* 2.7 45.6 + - + +
107F SER* 3.3 28.4 + - - -
110F SER* 3.7 11.4 - - - -
113F THR 3.9 2.3 + - - -
114F ASP 5.1 0.5 + - - -
116F GLN* 3.5 32.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLN* 4.2 18.4 - - - -
21F LEU* 3.5 39.9 - - + -
22F ARG 4.3 2.7 - - - -
23F CYS* 3.7 26.7 - - + -
39F LEU* 3.6 19.8 - - + +
40F TYR* 1.3 72.9 - - - +
42F TYR* 1.3 67.5 + - - +
52F PHE* 4.2 2.9 - - - -
53F LEU* 3.1 31.6 + - + +
54F ILE* 2.9 43.7 + - + +
56F PHE* 4.5 7.6 - + - -
78F ALA* 4.8 1.0 - - + +
87F SER* 3.1 26.6 + - - -
88F THR 4.8 0.2 - - - -
89F LEU* 3.7 37.5 - - + +
102F TYR* 4.6 8.5 - + + -
103F LEU 3.8 11.4 - - - -
104F CYS* 4.2 2.9 - - + -
122F THR* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LYS* 3.6 6.2 - - - -
116E LEU* 3.1 38.4 + - + -
40F TYR* 3.5 21.7 - - + -
41F TRP* 1.3 76.9 - - - +
43F ARG* 1.3 60.3 + - - +
50F LEU* 3.7 30.1 - - + -
51F GLU 3.4 4.5 - - - -
52F PHE* 3.8 37.5 - + + -
53F LEU* 3.9 7.5 - - - +
102F TYR* 3.5 6.1 - - - +
103F LEU* 2.8 41.8 + - + +
105F ALA* 3.9 3.8 - - + -
116F GLN* 2.7 31.9 + - - -
118F PHE* 3.5 21.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F TYR* 1.3 74.5 - - - +
44F GLN* 1.3 63.7 + - - +
45F SER* 5.9 1.1 - - - -
50F LEU* 3.7 1.4 - - - -
51F GLU* 2.7 82.0 + - + +
53F LEU* 3.8 15.0 - - + +
72F PRO* 3.5 23.8 - - - +
76F PHE* 3.4 16.6 - - - -
97F GLU* 3.3 24.2 + - - +
98F ASP* 3.4 8.3 + - - +
100F ALA* 3.8 21.3 - - + +
101F VAL 3.7 4.3 - - - -
102F TYR* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLN* 2.7 44.9 + - - -
46E HIS 5.4 1.6 + - - +
47E SER* 5.0 4.0 - - - +
103E TYR* 5.1 2.8 + - - -
118E PHE* 5.0 2.4 - - - -
43F ARG* 1.3 77.4 - - - +
45F SER* 1.3 68.4 + - - +
48F GLN 3.2 20.3 + - - +
49F GLY* 3.4 19.6 - - - +
50F LEU* 3.9 14.8 - - + +
51F GLU* 5.6 0.4 - - - -
100F ALA* 3.4 3.7 - - - +
101F VAL* 2.8 45.8 + - + +
103F LEU* 3.4 21.7 - - + +
----------------------------------------------------------
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