Contacts of the strand formed by residues 134 - 139 (chain E) in PDB entry 3KTM
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 LYS 134 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 4.2 6.1 - - - -
133E CYS* 1.3 76.4 - - - +
135E PHE* 1.3 71.4 + - - +
136E LEU* 3.9 23.6 + - + +
161E LYS* 6.1 1.3 - - - +
184E PHE 3.9 0.2 - - - +
185E VAL* 3.3 5.7 - - - -
186E CYS* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 4.8 12.6 - - - +
197A ALA* 3.8 27.6 - - + -
198A ALA* 3.7 29.8 - - - -
199A ALA* 3.9 10.3 - - + -
127E LEU* 4.2 16.6 - - + -
129E VAL* 3.7 19.3 - - + +
134E LYS* 1.3 79.6 - - - +
136E LEU* 1.3 72.5 + - - +
137E HIS* 3.9 22.2 - + - -
183E GLU* 3.7 24.5 - - + -
184E PHE 3.6 8.7 - - - -
185E VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E LYS* 4.0 26.7 - - + +
135E PHE* 1.3 86.9 - - - +
137E HIS* 1.3 63.4 + - - +
157E THR* 4.7 4.7 - - + -
161E LYS* 4.3 27.6 - - + +
183E GLU* 3.4 1.7 - - - +
184E PHE* 2.7 74.6 + - + +
186E CYS* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 4.0 17.5 - - + +
135E PHE* 3.9 19.4 - + + -
136E LEU* 1.3 80.0 - - - +
138E GLN* 1.3 61.3 + - - +
139E GLU* 3.0 33.0 + - - +
171E LEU* 4.2 7.0 - - + -
182E VAL 3.2 11.7 - - - +
183E GLU* 3.9 12.1 - - + -
184E PHE* 4.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E HIS* 1.3 76.0 - - - +
139E GLU* 1.3 68.6 + - - +
140E ARG* 4.0 25.6 + - + +
150E TRP* 4.4 5.5 - - + -
153E VAL* 3.0 32.3 - - + +
157E THR* 3.7 16.4 + - - +
171E LEU* 4.3 0.7 - - - +
181E GLY* 3.1 2.8 - - - -
182E VAL* 2.7 49.0 + - + +
184E PHE* 4.3 8.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 5.7 0.3 - - - +
137E HIS* 3.0 37.5 + - - +
138E GLN* 1.3 78.9 - - - +
140E ARG* 1.3 65.4 + - - +
141E MET* 3.6 23.3 + - + +
150E TRP* 5.2 0.2 - - - -
171E LEU* 4.0 11.5 - - + +
172E LEU* 4.0 19.1 - - + -
180E ARG 3.5 10.8 - - - +
181E GLY* 4.3 2.5 - - - -
----------------------------------------------------------
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