Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 2CLS
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 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS 3.4 3.2 + - - +
16A LEU* 3.4 16.5 - - + +
17A VAL 3.1 21.0 + - - -
85A SER* 3.4 4.7 - - - -
86A ASP* 1.3 80.8 - - - +
88A VAL* 1.3 64.5 + - - +
89A LEU* 4.1 1.1 - - + -
118A THR* 4.5 2.5 - - - -
119A ARG* 3.3 28.5 - - + +
121A LEU* 4.1 15.5 - - + -
187A CYS* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.3 13.9 - - + +
19A VAL* 3.8 24.5 - - + -
82A TYR* 4.3 19.7 - - + -
85A SER* 4.2 8.1 - - - +
87A ALA* 1.3 74.5 - - - +
89A LEU* 1.3 64.2 + - - +
90A LEU 3.6 0.7 + - - -
111A ILE* 3.6 43.1 - - + -
118A THR* 3.8 20.4 - - + -
119A ARG 2.9 10.3 + - - +
120A VAL* 3.4 4.4 - - + +
121A LEU 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.2 24.0 - - + -
17A VAL 2.7 11.4 + - - +
18A LEU* 3.4 20.5 - - + -
19A VAL 3.0 26.7 + - - +
87A ALA* 4.3 0.9 - - + -
88A VAL* 1.3 76.1 - - - +
90A LEU* 1.3 60.9 + - - +
91A CYS* 3.4 5.7 - - - -
121A LEU* 3.4 35.4 - - + -
123A ILE* 3.8 27.1 - - + -
179A ILE* 4.8 2.5 - - + -
180A PHE* 3.7 35.7 - - + -
183A ALA* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.7 8.7 - - + +
88A VAL 3.6 1.8 + - - -
89A LEU* 1.3 68.1 - - - +
91A CYS* 1.3 65.2 + - - +
104A LEU* 2.8 48.2 - - + +
107A TRP* 3.7 22.9 - - + -
108A ARG* 4.2 15.5 - - + +
111A ILE* 4.2 9.0 - - + -
120A VAL* 4.1 20.0 - - + -
121A LEU 2.9 13.8 + - - +
122A LEU* 3.4 12.6 - - + +
123A ILE 2.9 23.7 + - - -
159A LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 17.0 - - - -
19A VAL 2.8 13.7 + - - +
20A GLY* 3.5 18.4 - - - -
21A ASP 4.4 1.0 + - - -
24A CYS* 3.8 18.1 - - - -
26A LYS* 3.9 4.9 - - + -
29A MET* 3.9 24.9 - - - -
89A LEU* 3.4 19.7 - - - -
90A LEU* 1.3 81.0 - - - +
92A PHE* 1.3 63.6 + - - +
99A THR 4.9 1.0 - - - +
104A LEU* 4.0 1.6 - - - +
107A TRP* 5.3 0.2 - - - -
123A ILE* 3.2 14.6 - - - +
125A CYS* 4.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A CYS* 4.1 9.2 - - - -
91A CYS* 1.3 75.5 - - - +
93A ASP* 1.3 65.7 + - - +
94A ILE* 4.0 11.0 - - + -
99A THR* 3.3 26.9 - - - +
100A VAL* 3.0 28.5 - - + -
104A LEU* 3.9 8.3 - - + -
122A LEU* 3.8 31.0 - - + -
123A ILE 3.0 12.6 + - - +
124A GLY* 3.9 5.6 - - - -
125A CYS* 2.9 27.1 + - - +
147A ILE* 3.8 27.1 - - + -
155A ILE* 4.7 4.9 - - + -
164A TYR* 3.7 38.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A CYS* 3.7 13.6 - - - +
92A PHE* 1.3 74.4 - - - +
94A ILE* 1.3 60.5 + - - +
95A SER* 2.6 31.6 + - - -
96A ARG* 2.9 58.7 + - + +
99A THR* 2.8 19.0 + - - +
100A VAL* 4.9 0.2 - - - +
125A CYS 4.0 2.0 - - - -
126A LYS* 3.0 41.7 + - - +
129A LEU* 5.2 0.2 - - - +
147A ILE* 5.0 0.2 - - - +
----------------------------------------------------------
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