Contacts of the strand formed by residues 137 - 141 (chain A) in PDB entry 1OTH
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 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 3.5 3.0 + - - +
82A LEU* 3.5 19.2 - - + -
83A GLY 2.9 22.9 + - - -
135A ALA* 3.5 4.6 - - - +
136A ASP* 1.3 78.8 - - - +
138A VAL* 1.3 66.7 + - - +
157A ILE* 3.7 4.2 - - - +
158A PRO* 3.3 17.0 - - + +
160A ILE* 4.2 12.3 - - + -
338A MET* 4.6 0.9 - - - -
342A LEU* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.1 3.6 - - - -
83A GLY* 3.1 13.2 - - - +
85A ILE* 4.2 20.4 - - + -
131A LEU* 3.9 30.1 - - + -
135A ALA* 5.3 0.4 - - + -
137A ALA* 1.3 79.7 - - - +
139A LEU* 1.3 70.9 + - - +
140A ALA* 4.4 7.4 - - + -
151A LEU* 4.9 4.3 - - + -
157A ILE* 3.8 17.3 - - + -
158A PRO 2.9 6.3 + - - -
159A ILE* 3.5 24.5 - - + -
160A ILE* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.9 7.2 - - + +
83A GLY 2.9 7.5 + - - +
84A MET* 3.3 4.5 - - + -
85A ILE 2.8 24.9 + - - +
86A PHE* 3.8 31.9 - - + -
93A THR* 4.1 4.5 - - + -
97A THR* 3.8 29.6 - - + +
138A VAL* 1.3 74.2 - - - +
140A ALA* 1.3 64.2 + - - +
160A ILE* 3.3 32.5 - - + +
162A GLY* 3.9 14.4 - - - -
170A ILE* 4.1 11.2 - - + -
334A ILE* 4.0 14.1 - - + -
338A MET* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.2 18.4 - - + +
138A VAL* 4.1 5.1 - - + -
139A LEU* 1.3 76.2 - - - +
141A ARG* 1.3 57.6 + - - +
142A VAL* 3.7 13.7 + - + -
148A LEU* 3.7 28.3 - - + +
151A LEU* 4.2 15.3 - - + -
159A ILE* 5.4 0.7 - - + -
160A ILE 3.0 8.5 + - - +
161A ASN* 4.2 0.2 - - - +
162A GLY* 2.8 24.5 + - - -
163A LEU 3.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE 2.8 9.4 + - - +
86A PHE* 3.7 31.5 - - + -
87A GLU* 2.8 33.5 + - - +
88A LYS* 3.8 26.0 - - + +
89A ARG 2.9 24.5 + - - -
90A SER* 3.6 2.9 - - - -
93A THR* 2.9 24.1 + - - -
139A LEU* 4.3 1.8 - - - +
140A ALA* 1.3 70.1 - - - +
142A VAL* 1.3 60.9 + - - +
162A GLY* 2.9 26.1 + - - +
163A LEU* 3.3 26.3 - - + +
168A HIS* 3.6 1.4 + - - -
268A MET* 3.5 11.1 - - - +
355A PAO 2.8 46.0 + - - -
----------------------------------------------------------
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