Contacts of the strand formed by residues 138 - 143 (chain A) in PDB entry 1II7
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 LEU 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.3 22.9 - - + -
3A PHE* 5.3 0.4 - - + -
43A PHE* 3.8 32.8 - - + -
134A VAL* 3.7 3.5 - - - +
135A TYR* 2.8 44.6 + - + +
136A LYS 4.2 1.6 - - - +
137A ASP* 1.3 77.1 + - - +
139A GLU* 1.3 74.2 + - - +
140A ILE* 4.8 3.1 - - + +
167A ASN* 3.1 49.4 - - - +
168A ALA* 3.7 8.3 - - - -
169A ILE* 4.1 13.5 - - + -
261A PHE* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 5.2 7.5 - - - +
132A LYS* 4.1 13.1 + - + +
133A GLY 3.4 9.4 - - - +
134A VAL* 4.7 10.4 - - + +
137A ASP 5.6 1.8 - - - +
138A LEU* 1.3 81.0 - - - +
140A ILE* 1.3 63.5 + - - +
141A HIS* 2.9 30.7 + - + +
165A THR* 3.1 25.0 - - + +
167A ASN 3.0 12.4 + - - +
168A ALA* 3.2 6.7 - - + +
169A ILE 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.0 22.4 - - + -
45A LEU* 4.0 15.9 - - + -
79A PHE* 3.4 46.2 - - + -
107A ILE* 3.6 22.3 - - + +
132A LYS* 3.6 3.5 - - - -
133A GLY* 2.8 41.0 + - - +
134A VAL 4.7 0.7 - - - +
135A TYR* 4.9 6.1 - - + -
138A LEU* 4.8 3.8 - - + +
139A GLU* 1.3 78.1 - - - +
141A HIS* 1.3 68.1 + - - +
169A ILE* 3.6 21.5 - - + +
171A MET* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.1 3.1 - - - -
132A LYS* 3.5 39.0 - - + +
139A GLU* 2.9 37.7 + - + +
140A ILE* 1.3 79.4 - - - +
142A GLY* 1.3 59.4 + - - +
162A PHE* 3.8 12.4 - - + +
163A ARG 3.1 26.4 + - - -
164A PRO* 4.2 3.6 - - + -
165A THR* 4.4 2.9 - - + +
168A ALA* 4.4 2.4 - - + +
169A ILE 2.7 14.1 + - - +
170A LEU* 3.9 5.2 - - + -
171A MET* 2.7 28.8 + - - +
199A TYR* 2.4 36.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.8 0.4 - - - -
107A ILE* 3.7 16.8 - - - +
108A GLY* 3.4 15.9 + - - -
130A LEU* 4.1 2.6 - - - +
131A VAL 4.6 1.3 + - - +
132A LYS* 5.6 0.4 - - - +
141A HIS* 1.3 79.9 - - - +
143A MET* 1.3 62.0 + - - +
162A PHE* 3.3 23.8 - - - -
170A LEU* 4.2 3.4 - - - -
171A MET* 3.0 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.6 24.1 - - - +
108A GLY* 4.1 10.3 - - - -
109A MET* 4.7 14.6 - - + +
130A LEU* 5.8 0.7 - - + -
142A GLY* 1.3 76.8 - - - +
144A LYS* 1.3 73.9 + - + +
146A MET* 3.9 16.8 - - + -
150A TRP* 3.8 26.2 - - + -
151A PHE* 3.8 29.6 - - + -
158A LEU* 4.0 12.8 - - + -
161A LEU* 4.1 19.7 - - - -
162A PHE* 3.6 12.1 - - + -
171A MET 3.4 5.8 + - - +
172A LEU* 4.1 15.5 - - + +
173A HIS 4.3 0.5 + - - -
174A GLN* 4.8 1.3 - - - +
----------------------------------------------------------
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