Contacts of the helix formed by residues 102 - 115 (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 SER 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 1.3 79.8 - - - +
103A ALA* 1.3 57.6 - - - +
104A LEU 3.5 0.7 - - - -
105A LYS* 3.3 12.8 - - - +
106A LYS* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 3.6 26.2 - - - +
98A GLU 3.4 21.5 + - - +
99A THR 3.6 5.4 - - - +
101A ASP 3.2 1.8 - - - -
102A SER* 1.3 76.0 - - - +
104A LEU* 1.3 61.3 + - - +
105A LYS 3.2 0.5 + - - -
106A LYS* 3.3 11.8 + - + +
107A TRP* 2.9 34.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 2.8 41.5 - - + +
91A CYS 4.0 9.0 - - - +
92A PHE* 3.9 13.0 - - + -
99A THR 3.4 14.8 - - - +
100A VAL* 3.1 33.3 + - + +
101A ASP 4.7 0.4 - - - +
103A ALA* 1.3 77.2 - - - +
105A LYS* 1.3 53.4 + - - +
107A TRP* 4.2 3.8 - - + -
108A ARG* 2.9 28.8 + - - +
122A LEU* 3.8 15.0 - - + -
155A ILE* 3.7 27.6 - - + -
159A LEU* 3.6 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP 4.5 3.8 + - - +
102A SER* 3.3 18.9 + - - +
103A ALA 3.2 1.0 - - - -
104A LEU* 1.3 73.8 - - - +
106A LYS* 1.3 59.2 + - - +
108A ARG* 3.2 2.5 + - - +
109A THR* 2.8 38.2 + - - +
159A LEU* 4.2 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 5.3 1.8 - - - +
70A GLY 5.4 0.6 + - - -
72A PRO* 4.7 11.5 - - - +
75A ASP* 3.3 35.4 + - - -
102A SER 3.2 9.8 + - - +
103A ALA* 3.3 14.4 - - + +
105A LYS* 1.3 76.2 - - - +
107A TRP* 1.3 107.5 + - + +
109A THR* 3.5 5.9 + - - -
110A GLU* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.9 18.6 - - + -
20A GLY* 3.4 34.1 - - - -
21A ASP* 2.8 28.8 + - - +
69A SER 4.3 0.4 - - - -
70A GLY* 3.5 22.0 - - - -
78A ARG* 3.6 46.7 - - - -
82A TYR* 4.8 0.4 - - - -
90A LEU* 3.7 26.2 - - + -
99A THR 4.9 0.4 - - - -
103A ALA* 2.9 36.2 + - + +
104A LEU* 3.8 6.7 - - + +
106A LYS* 1.3 95.9 - - + +
108A ARG* 1.3 63.2 + - - +
110A GLU* 3.4 16.4 + - - +
111A ILE* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.2 4.4 - - + +
104A LEU 2.9 19.2 + - - +
105A LYS* 3.2 4.9 + - - +
107A TRP* 1.3 76.0 - - - +
109A THR* 1.3 57.4 + - - +
111A ILE* 3.5 9.2 + - - +
112A LEU* 3.0 62.7 + - + +
115A CYS 5.8 0.4 + - - -
116A PRO* 5.2 4.4 + - - +
118A THR 4.7 6.5 + - - -
120A VAL* 3.7 39.6 - - - +
159A LEU* 2.8 47.9 + - + +
160A GLY* 4.3 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 2.8 20.0 + - - +
106A LYS* 3.7 6.1 - - - -
108A ARG* 1.3 74.8 - - - +
110A GLU* 1.3 56.2 + - - +
112A LEU* 3.6 11.4 - - + +
113A ASP* 2.7 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP* 3.8 10.5 - - - +
78A ARG* 2.9 36.5 + - - +
79A PRO* 4.4 14.0 - - + +
82A TYR* 2.4 35.7 + - + +
106A LYS* 3.1 20.6 + - + +
107A TRP* 3.4 19.2 + - + +
109A THR* 1.3 77.1 - - - +
111A ILE* 1.3 61.7 + - - +
113A ASP* 3.4 7.5 + - - +
114A TYR* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.1 10.8 - - + -
82A TYR* 4.5 20.0 - - + +
88A VAL* 3.6 45.3 - - + -
90A LEU* 4.2 12.8 - - + -
107A TRP 3.2 22.7 + - - +
108A ARG* 3.8 12.1 - - - +
110A GLU* 1.3 76.2 - - - +
112A LEU* 1.3 63.5 + - - +
114A TYR* 3.2 5.5 + - + +
115A CYS 3.1 24.8 + - - +
118A THR* 4.5 13.9 - - + +
120A VAL* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.0 42.7 + - + +
109A THR* 3.6 12.1 - - + +
111A ILE* 1.3 76.1 - - - +
113A ASP* 1.3 63.6 + - - +
115A CYS 3.3 12.4 + - - -
116A PRO* 3.4 47.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 2.7 45.6 + - - +
110A GLU* 3.7 7.8 + - - +
112A LEU* 1.3 74.0 - - - +
114A TYR* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.7 31.2 - - + -
80A LEU* 5.7 0.9 - - - -
82A TYR* 3.6 42.2 - + + -
83A SER* 2.9 35.4 - - - -
84A ASP 5.1 1.3 - - - -
110A GLU 3.1 9.4 + - - +
111A ILE* 3.2 8.9 + - + +
113A ASP* 1.3 79.4 - - - +
115A CYS* 1.3 77.7 + - + +
118A THR* 4.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 5.8 0.3 + - - -
111A ILE* 3.1 12.4 + - - +
112A LEU 3.3 3.5 + - - -
114A TYR* 1.3 100.8 - - + +
116A PRO* 1.3 67.6 - - - +
117A SER* 3.1 35.7 + - - -
118A THR* 3.3 22.7 + - - +
----------------------------------------------------------
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