Contacts of the strand formed by residues 108 - 113 (chain A) in PDB entry 1KEK
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 VAL 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR 3.5 8.5 + - - +
82A THR* 2.8 32.9 - - - +
83A THR 3.3 1.6 + - - -
106A PRO 3.9 3.6 + - - +
107A GLY* 1.3 79.6 - - - +
109A PHE* 1.3 67.3 + - - +
110A HIS* 3.4 31.4 - - + +
156A ALA* 3.9 14.6 - - + +
157A HIS* 3.7 37.7 - - + +
160A ALA* 3.6 22.7 - - + -
167A PHE* 3.2 9.2 - - + +
169A HIS* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 4.9 4.9 - - + -
71A VAL* 4.0 21.3 - - + -
83A THR* 3.6 23.6 - - + -
85A THR* 5.1 2.0 - - + -
90A LEU* 4.3 8.1 - - + -
93A MET* 3.5 31.9 - - + -
97A MET* 3.6 33.4 - - + -
100A ILE* 3.9 16.4 - - + -
107A GLY* 5.5 0.7 - - - -
108A VAL* 1.3 81.0 - - - +
110A HIS* 1.3 62.4 + - - +
111A VAL* 3.9 11.3 + - + -
138A PHE* 3.7 29.8 - + + -
167A PHE 2.9 9.4 + - - +
168A MET* 3.5 5.1 - - + +
169A HIS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.5 15.9 - - - +
18A ALA* 3.5 16.1 - - + +
36A MET* 3.9 9.1 - - - +
82A THR* 3.2 26.7 - - + +
83A THR 2.9 7.1 + - - -
84A PHE* 3.2 21.4 - + + -
85A THR* 3.0 22.9 + - - +
108A VAL* 3.4 14.1 - - + +
109A PHE* 1.3 69.0 - - - +
111A VAL* 1.3 61.1 + - - +
153A ALA* 4.0 9.5 - - - +
157A HIS* 2.9 35.4 + - - -
169A HIS* 3.1 40.7 - + + +
171A PHE* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.1 18.4 - - + +
86A ALA* 4.2 3.1 - - - -
90A LEU* 4.3 11.4 - - + -
109A PHE* 4.3 9.4 - - + -
110A HIS* 1.3 77.4 - - - +
112A THR* 1.3 74.1 + - - +
113A ALA 3.9 0.7 - - - +
129A ASP* 4.0 9.0 - - - +
130A ILE* 3.8 24.2 - - + -
168A MET* 3.6 40.8 - - + -
169A HIS 2.8 12.9 + - - +
170A PHE* 3.3 6.2 - - + +
171A PHE* 3.2 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.3 29.8 - - - +
32A PRO* 3.2 30.1 - - - +
33A SER* 3.3 18.5 - - - -
36A MET* 3.7 11.9 - - + -
85A THR 3.1 3.6 + - - -
86A ALA* 3.1 18.7 - - - +
110A HIS 4.3 0.2 + - - -
111A VAL* 1.3 71.1 - - - +
113A ALA* 1.3 64.0 + - - +
114A ARG* 3.9 1.2 - - - +
129A ASP* 3.6 0.9 - - - +
171A PHE* 3.4 21.5 - - + -
173A GLY* 4.1 5.8 - - - -
177A SER* 3.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 3.5 3.3 + - - -
112A THR* 1.3 69.4 - - - +
114A ARG* 1.3 57.6 + - - +
125A GLY* 3.2 10.4 - - - -
126A ASP 3.1 18.0 + - - +
127A HIS* 3.9 17.0 - - + -
129A ASP* 3.3 14.4 - - - +
130A ILE* 3.8 16.4 - - + -
170A PHE* 4.4 5.4 - - + -
171A PHE 2.8 18.1 + - - +
172A ASP* 4.3 0.6 - - - -
173A GLY* 2.8 25.2 + - - +
----------------------------------------------------------
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