Contacts of the strand formed by residues 116 - 120 (chain M) in PDB entry 1OZT
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 THR 116 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M VAL* 3.2 3.9 - - - -
48M HIS* 2.6 36.3 + - - +
50M PHE 2.7 24.9 + - - -
51M GLY* 3.2 13.2 - - - -
52M ASP 3.9 2.8 + - - -
53M ASN* 5.9 0.7 - - - +
60M ALA* 3.7 15.0 - - + +
115M ARG* 1.3 74.3 + - - +
117M LEU* 1.3 70.7 + - - +
118M VAL* 3.7 9.8 + - + -
146M CYS* 3.6 20.0 - - + -
147M GLY 3.4 14.8 + - - +
148M VAL* 4.1 5.0 - - - +
149M ILE* 4.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M CYS* 3.7 20.9 - - - -
8M LEU* 3.3 8.4 - - + +
18M ILE* 3.8 35.9 - - + -
20M PHE* 3.9 14.4 - - + -
45M PHE* 3.9 31.4 - - + -
46M ARG 3.5 20.6 - - - +
47M VAL* 4.1 13.0 - - + +
84M LEU* 4.4 7.4 - - + -
115M ARG 4.1 0.8 + - - -
116M THR* 1.3 73.6 - - - +
118M VAL* 1.3 61.8 + - - +
146M CYS* 3.0 25.5 - - - +
147M GLY 3.0 8.8 + - - -
149M ILE* 4.1 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LEU* 4.8 0.9 - - - -
44M GLY 3.8 0.3 - - - +
45M PHE* 3.5 7.8 - - - -
46M ARG 2.7 34.1 + - - -
48M HIS* 3.2 35.4 - - + +
57M CYS* 5.1 0.4 - - + -
60M ALA* 4.6 4.7 - - + -
116M THR* 3.7 17.7 - - + -
117M LEU* 1.3 81.4 - - - +
119M VAL* 1.3 67.8 + - - +
120M HIS* 3.8 15.7 - - + +
143M ARG* 3.7 32.1 - - + -
145M ALA 3.5 11.4 - - - +
146M CYS* 3.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LEU* 5.0 6.2 - - + +
14M VAL* 3.8 28.0 - - + -
35M ILE* 4.4 18.6 - - + -
38M LEU* 4.5 9.4 - - + -
43M HIS* 3.9 20.0 - - + -
44M GLY 3.3 9.9 - - - +
45M PHE* 4.6 4.9 - - + +
87M VAL* 4.2 14.6 - - + -
118M VAL* 1.3 78.2 - - - +
120M HIS* 1.3 65.0 + - - +
144M LEU* 3.0 21.9 + - + +
145M ALA* 3.1 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M HIS* 2.9 29.3 + - - +
44M GLY 2.7 25.9 + - - +
46M ARG* 3.2 28.3 + - + +
48M HIS* 3.1 36.7 + + - -
63M HIS* 4.8 0.7 - - - -
118M VAL* 3.8 10.7 - - + +
119M VAL* 1.3 78.3 - - - +
121M GLU* 1.3 60.3 + - - +
122M LYS 3.3 2.9 + - - +
140M ALA* 3.3 26.3 - - + +
141M GLY 3.5 16.7 + - - -
142M SER 3.5 2.9 - - - -
143M ARG* 4.0 21.6 - - + +
144M LEU* 3.8 4.4 - - - +
----------------------------------------------------------
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