Contacts of the strand formed by residues 133 - 140 (chain B) in PDB entry 2KAI
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 GLY 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 1.3 74.3 - - - +
134B SER* 1.3 65.0 + - - +
135B THR* 3.8 1.9 + - - -
161B THR* 4.1 14.5 - - - +
162B LEU 2.7 17.6 + - - -
163B LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 2.7 44.0 + - - +
132B LEU 3.1 1.2 + - - -
133B GLY* 1.3 81.0 - - - +
135B THR* 1.3 60.8 + - - +
161B THR* 3.4 5.6 - - - +
162B LEU* 2.9 37.7 + - - -
201B CYS* 4.2 20.3 - - - +
202B ASN* 4.8 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 3.8 2.5 + - - -
134B SER* 1.3 76.0 - - - +
136B CYS* 1.3 61.6 + - - +
159B GLN* 3.4 36.5 - - + +
160B LEU 3.6 6.3 - - - +
161B THR* 4.8 4.3 + - - +
200B ILE 4.1 0.7 - - - +
201B CYS* 3.8 0.2 - - - -
202B ASN* 3.5 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER 4.3 0.2 - - - -
135B THR* 1.3 77.0 - - - +
137B GLU* 1.3 57.2 + - - +
159B GLN* 3.1 9.1 - - - +
160B LEU* 2.7 43.5 + - + +
162B LEU* 3.7 28.5 - - - -
183B ALA* 4.9 0.7 - - + -
199B LEU* 3.5 26.0 - - + -
200B ILE 3.2 6.1 - - - +
201B CYS* 2.1 43.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 5.0 7.3 - - - +
29A TRP* 5.0 13.0 - - - -
136B CYS* 1.3 73.7 - - - +
138B ALA* 1.3 67.5 + - - +
139B SER* 5.4 1.7 + - - -
157B CYS* 3.9 22.8 - - + +
158B VAL 3.3 12.8 - - - +
159B GLN* 3.1 26.5 - - - +
198B PRO 3.8 1.7 - - - +
199B LEU* 3.7 5.9 - - - +
200B ILE* 2.8 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.0 2.0 - - + +
137B GLU* 1.3 75.6 - - - +
139B SER* 1.3 62.9 + - - +
157B CYS* 3.3 4.2 - - - +
158B VAL* 2.8 44.1 + - + +
160B LEU* 4.0 9.4 - - + +
190B THR* 3.5 31.9 - - + -
198B PRO 3.7 10.8 - - - +
199B LEU* 4.1 6.3 - - + +
213B THR* 5.2 1.1 - - - +
228B TYR* 4.7 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.9 11.2 - - - +
22A CYS* 3.9 5.6 - - - -
27A HIS* 5.1 1.7 - - - +
29A TRP* 4.3 9.6 - - - -
30A GLN* 2.8 29.6 + - - -
137B GLU* 5.4 2.0 + - - -
138B ALA* 1.3 75.6 - - - +
140B GLY* 1.3 58.1 + - - +
155B ILE* 4.3 3.4 - - - -
156B GLN 3.3 8.3 - - - -
157B CYS* 3.4 24.7 - - - +
190B THR* 5.5 0.2 - - - +
194B ASP* 4.3 5.2 - - - +
197B GLY* 4.5 13.5 - - - -
198B PRO* 4.0 12.5 + - - +
213B THR* 5.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 3.7 - - - +
30A GLN* 4.3 11.4 - - - -
139B SER* 1.3 78.7 - - - +
141B TRP* 1.3 62.7 + - - -
142B GLY 3.4 1.4 + - - +
152B PRO* 4.9 0.5 - - - +
155B ILE* 3.7 9.7 - - - +
156B GLN* 3.0 30.8 + - - +
194B ASP* 3.2 18.7 - - - +
----------------------------------------------------------
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