Contacts of the strand formed by residues 136 - 143 (chain B) in PDB entry 5KC6
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 TRP 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B MET* 3.5 4.5 - - - -
133B LEU 2.8 29.7 + - - +
134B ASN* 3.2 25.3 + - + -
135B GLY* 1.3 82.7 + - - +
137B PRO* 1.3 78.7 - - + +
202B HIS* 3.2 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 4.1 10.3 - - - +
131B LEU 3.6 7.2 - - - +
132B MET* 3.3 15.9 - - + -
135B GLY 4.5 1.1 - - - +
136B TRP* 1.3 100.4 - - + +
138B VAL* 1.3 61.6 + - - +
139B ILE 4.8 1.3 - - - +
140B SER* 4.9 2.7 - - - +
172B GLU* 3.8 23.1 - - - +
202B HIS* 3.2 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 2.9 18.9 + - + +
132B MET 4.7 0.4 - - - -
133B LEU* 3.7 22.7 - - + +
137B PRO* 1.3 74.8 - - - +
139B ILE* 1.3 73.5 + - + +
157B VAL* 4.6 2.2 - - + -
159B ILE* 3.8 21.8 - - + -
202B HIS* 3.5 30.5 - - + +
67C ILE* 4.2 16.3 - - - +
90C LEU* 3.5 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 4.0 13.2 - - + -
130B SER* 3.2 6.6 + - - -
131B LEU* 3.1 41.3 + - + -
137B PRO* 5.5 0.2 - - - -
138B VAL* 1.3 88.1 + - + +
140B SER* 1.3 64.7 + - - +
155B ASN* 3.9 15.7 - - + +
156B GLY* 3.8 26.5 - - - +
157B VAL* 3.5 38.6 - - + -
67C ILE* 4.4 7.4 - - + -
182C TYR* 5.6 1.6 - - - -
184C THR* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 4.9 0.9 - - - -
128B GLN* 3.3 22.9 + - - -
129B VAL 3.3 6.1 - - - -
130B SER* 2.6 22.6 + - - -
137B PRO* 4.9 3.5 - - - +
139B ILE* 1.3 74.5 - - - +
141B ALA* 1.3 61.6 + - - +
142B PHE* 4.2 8.8 - - - -
155B ASN* 3.0 24.2 + - - -
172B GLU* 4.7 0.7 + - - -
119C VAL* 5.3 1.9 - - - +
182C TYR* 3.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 3.9 11.9 - - + -
128B GLN* 3.3 6.2 - - - +
129B VAL 2.7 28.9 + - - +
140B SER* 1.3 74.9 - - - +
142B PHE* 1.3 68.8 + - - +
153B ALA* 3.5 11.4 - - + +
154B SER 3.4 42.6 - - - +
155B ASN* 4.1 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE 3.7 6.7 - - - +
128B GLN* 3.4 44.9 - - + -
140B SER* 4.2 5.6 - - - -
141B ALA* 1.3 82.7 - - - +
143B ALA* 1.3 63.5 + - - +
152B ALA 3.4 5.9 - - - +
153B ALA* 3.4 14.8 - - - -
154B SER 4.7 0.2 + - - -
173B ARG* 4.5 12.1 - - - -
119C VAL* 4.5 9.0 - - + -
149C THR* 4.0 6.7 - - - +
150C ARG* 3.5 64.0 - - + +
151C GLU* 6.0 0.5 - - - -
182C TYR* 3.7 40.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 4.1 10.8 - - + -
126B THR* 2.8 23.9 + - - -
127B ILE* 3.4 37.4 + - + +
142B PHE* 1.3 80.1 - - - +
144B GLY* 1.3 60.2 + - - +
151B GLU* 4.2 11.4 - - + -
152B ALA 4.1 5.8 - - - -
153B ALA 3.9 15.9 - - - +
149C THR* 4.0 3.1 + - - -
150C ARG 5.3 0.4 - - - -
----------------------------------------------------------
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