Contacts of the strand formed by residues 38 - 44 (chain G) 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 TYR 38 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 3.1 28.9 + - - -
70B ARG* 3.4 44.6 - - - +
73B ALA* 3.4 18.6 - - + +
77B ARG* 3.3 41.5 - - - -
37G GLU* 1.3 72.9 - - - +
39G VAL* 1.3 61.8 + - - +
40G TYR* 3.7 18.4 - + + -
55G HIS* 3.6 15.0 - + + -
56G GLY* 3.4 17.9 - - - +
57G LEU* 3.7 22.0 - - + -
106G VAL* 3.4 10.7 - - - +
107G TRP* 2.6 37.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G HIS* 3.7 28.3 - - + +
28G ILE* 3.9 13.9 - - + -
38G TYR* 1.3 73.2 - - - +
40G TYR* 1.3 58.9 + - - +
41G TRP* 4.1 8.1 - - + +
54G ILE 4.1 0.2 - - - +
55G HIS* 3.3 18.5 - - - -
56G GLY 2.8 20.4 + - - +
78G LEU* 3.4 13.4 - - + +
80G ILE* 4.5 10.8 - - + -
84G ARG* 4.5 8.3 - - - +
87G SER* 3.4 28.0 - - - +
104G CYS* 4.1 16.8 - - - -
105G ILE 3.8 3.4 - - - +
106G VAL* 5.0 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 2.9 36.3 + - - -
38G TYR* 3.7 14.4 - - + -
39G VAL* 1.3 73.6 - - - +
41G TRP* 1.3 62.2 + - - +
42G TYR* 3.6 35.0 - + + -
52G TYR* 3.7 25.8 - + - -
54G ILE 3.8 2.9 - - - -
55G HIS* 3.5 32.0 + + + -
104G CYS* 3.5 5.7 - - - +
105G ILE* 2.8 43.3 + - + +
107G TRP* 3.5 34.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.8 23.6 - - - -
21G LEU* 3.8 35.4 - - + -
22G PRO 4.2 3.6 - - - -
23G CYS* 3.8 11.4 - - + -
39G VAL* 4.1 9.2 - - + +
40G TYR* 1.3 81.8 - - - +
42G TYR* 1.3 66.2 + - - +
52G TYR* 4.1 1.4 - - - -
53G ILE* 3.0 32.0 + - + +
54G ILE 3.0 16.0 + - - +
78G LEU* 3.4 32.4 - - + +
87G SER* 4.3 2.1 + - - -
88G THR 5.0 0.4 - - - -
89G LEU* 3.6 42.2 - - + -
102G TYR* 3.7 28.5 - + + -
103G TYR 3.4 16.6 - - - -
104G CYS* 3.6 21.3 - - + -
122G THR* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G TYR* 3.6 31.2 - + + -
41G TRP* 1.3 77.6 - - - +
43G ARG* 1.3 59.9 + - - +
50G PRO* 4.5 15.3 - - + -
51G GLN 3.3 18.4 - - - -
52G TYR* 3.7 32.3 - + + +
53G ILE* 3.6 4.5 - - - +
102G TYR* 3.5 3.3 - - - +
103G TYR* 2.7 36.3 + - + +
105G ILE* 3.7 24.2 - - + -
107G TRP* 6.3 0.4 - + - -
116G LEU* 4.1 31.6 - - + +
118G PHE* 4.3 16.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TYR* 1.3 73.7 - - - +
44G GLN* 1.3 61.4 + - - +
45G ILE* 4.4 15.9 - - + +
49G GLY 4.4 0.2 - - - +
50G PRO* 3.5 4.1 - - - +
51G GLN* 2.8 69.0 + - + +
53G ILE* 3.7 17.5 - - + +
75G MET* 4.9 12.3 - - - +
91G LEU* 5.0 3.6 - - - +
97G ARG* 4.1 16.5 + - - +
98G ASP* 2.8 33.5 + - - +
100G ALA* 4.3 9.2 - - + -
101G VAL 3.4 7.2 - - - +
102G TYR* 3.1 37.6 + - + -
103G TYR* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ARG* 1.3 75.5 - - - +
45G ILE* 1.3 60.8 + - - +
46G HIS 3.6 20.1 + - - +
47G SER* 4.2 6.8 + - - +
48G GLN 2.8 29.3 + - - +
49G GLY 5.0 0.9 - - - -
50G PRO* 3.7 26.7 - - + +
100G ALA* 3.4 4.4 - - - +
101G VAL* 3.1 43.1 + - + +
103G TYR* 3.9 22.5 + - + -
118G PHE* 4.4 5.9 - - - -
----------------------------------------------------------
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