Contacts of the strand formed by residues 130 - 135 (chain A) in PDB entry 2OTM
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 SER 130 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR 3.0 4.4 + - - -
94A ARG* 3.0 31.8 + - - -
95A LEU 3.0 22.2 + - - -
129A HIS* 1.3 76.9 - - - +
131A ARG* 1.3 64.3 + - - +
26C TYR* 4.7 0.2 - - - -
27C GLU 3.4 7.9 - - - -
29C TYR* 4.0 3.4 - - - -
30C SER* 2.7 38.5 + - - -
37C MSE 3.7 2.4 - - - +
39C SER* 3.3 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 4.3 3.1 - - - +
95A LEU* 3.1 15.3 - - + +
109A PRO* 3.2 26.2 + - - +
112A LEU* 3.6 23.6 - - - +
113A ASP* 3.0 31.3 + - - +
116A SER* 3.0 26.9 + - - -
129A HIS* 4.1 7.6 - - + -
130A SER* 1.3 79.5 - - - +
132A MSE 1.3 67.2 + - - +
156A ACT 2.8 41.4 + - - +
24C GLY* 4.1 2.2 - - - -
26C TYR* 3.2 32.3 - - + -
39C SER* 3.0 20.6 + - - -
40C GLY 3.9 1.0 + - - -
148C TYR* 3.5 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.0 30.7 - - - +
95A LEU 3.0 5.5 + - - +
96A GLU* 3.1 36.3 - - + +
97A GLY 3.1 23.2 + - - -
112A LEU* 3.9 6.4 - - - +
131A ARG* 1.3 74.5 - - - +
133A ILE* 1.3 61.7 + - - +
134A TRP* 3.6 30.3 - - + -
156A ACT 5.0 0.2 - - - -
96C GLU* 3.3 27.1 - - + +
134C TRP* 3.7 11.4 - - + -
148C TYR* 3.4 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLY 3.4 6.3 - - - +
99A LEU* 4.4 5.4 - - + -
108A HIS* 3.6 35.0 - - + +
109A PRO* 3.7 26.2 - - + -
112A LEU* 3.7 23.8 - - + -
132A MSE 1.3 75.2 - - - +
134A TRP* 1.3 76.0 + - - +
156A ACT 3.7 33.0 + - + +
98C VAL* 5.1 1.7 - - - +
136C ASN* 4.5 1.2 - - - +
140C PRO* 4.0 17.0 - - + -
146C LEU* 4.5 6.8 - - + +
148C TYR* 3.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 3.7 40.8 - - + -
97A GLY 3.0 29.5 + - - +
98A VAL* 3.4 12.6 - - + -
99A LEU* 3.0 24.8 + - - +
108A HIS* 5.1 0.7 - - - -
132A MSE 3.6 33.1 - - + +
133A ILE* 1.3 81.4 + - - +
135A THR* 1.3 65.2 + - - +
136A ASN* 4.0 13.2 - - - +
132B MSE 3.9 6.7 - - + -
134B TRP* 3.5 35.4 - + - -
98C VAL* 3.8 16.9 - - + +
134C TRP* 3.4 39.9 - + - -
136C ASN* 3.3 24.2 - - - +
148C TYR* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU 3.1 5.6 - - - -
101A VAL* 3.4 36.6 - - + -
108A HIS* 3.5 26.5 - - + +
134A TRP* 1.3 74.4 - - - +
136A ASN* 1.3 71.2 + - - +
137A PRO* 4.6 0.2 - - - +
136C ASN* 3.1 20.9 + - - +
137C PRO* 3.4 10.9 - - - +
138C VAL* 2.7 42.0 + - + +
----------------------------------------------------------
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