Contacts of the strand formed by residues 208 - 215 (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 MET 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU 5.6 0.7 - - - +
123B LEU 5.0 2.2 - - - +
124B PRO* 3.8 13.2 - - + -
125B THR* 3.3 40.2 - - - +
127B GLN* 3.6 43.1 - - + +
200B ILE* 3.7 2.0 - - - -
201B CYS 2.9 37.3 + - - +
202B ASN 3.3 4.0 - - - +
203B GLY* 1.3 79.2 - - - +
209B TRP* 1.3 64.3 + - - +
210B GLN* 3.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.6 34.1 - - + -
47A VAL* 4.4 5.8 - - + -
53A LEU* 3.7 30.5 - - + -
121B LEU* 3.5 57.5 - - + +
122B GLU 3.9 9.8 + - - +
123B LEU* 3.2 28.0 - - + -
124B PRO* 3.1 30.3 - - - +
198B PRO* 3.8 12.1 - - + +
199B LEU 3.7 12.6 - - - -
200B ILE* 3.9 8.4 - - - +
203B GLY 4.1 0.8 + - - -
208B MET* 1.3 69.7 - - - +
210B GLN* 1.3 65.3 + - - +
211B GLY 2.9 27.5 + - - +
212B ILE* 4.1 7.2 - - + -
231B LEU* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.5 17.3 - - - +
127B GLN 3.3 26.4 + - - +
128B GLU* 4.2 1.6 - - - -
129B PRO* 3.4 43.8 - - + +
181B LEU* 3.5 13.6 - - + +
199B LEU 2.8 15.5 + - - +
201B CYS* 3.9 18.2 + - - +
208B MET* 3.2 31.2 + - - +
209B TRP* 1.3 74.2 - - - +
211B GLY* 1.3 54.5 + - - +
230B LYS* 4.0 2.1 - - + +
231B LEU* 3.1 26.7 + - - +
232B ILE* 4.3 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.1 5.6 - - - -
198B PRO* 3.5 0.3 - - - +
199B LEU* 2.8 40.2 + - - +
209B TRP* 2.9 19.3 + - - -
210B GLN* 1.3 78.4 - - - +
212B ILE* 1.3 62.8 + - - +
228B TYR* 4.5 1.6 - - - -
229B THR 3.1 13.7 - - - -
231B LEU* 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.4 48.0 - - + +
54A THR* 4.1 7.4 - - - +
55A ALA* 4.3 11.4 - - + -
102B ASP 4.5 3.6 - - - +
103B LEU* 3.9 9.2 - - + -
196B GLY* 3.8 21.8 - - - +
197B GLY 3.2 10.1 - - - +
209B TRP* 4.1 12.6 - - + -
211B GLY* 1.3 79.0 - - - +
213B THR* 1.3 68.8 + - - +
214B SER* 3.3 0.9 + - - -
228B TYR* 3.4 5.3 - - - +
229B THR* 2.8 49.4 + - - +
231B LEU* 4.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 4.0 0.2 - - - +
57A HIS* 4.0 2.4 - - - -
138B ALA* 5.2 0.9 - - - +
139B SER 5.4 0.9 + - - -
190B THR* 3.7 33.8 - - + +
194B ASP* 3.5 32.6 + - - +
195B SER* 3.2 8.2 - - - +
196B GLY 3.0 21.9 + - - -
197B GLY* 3.1 17.2 + - - -
198B PRO 4.6 2.9 + - - -
212B ILE* 1.3 75.0 - - - +
214B SER* 1.3 60.7 + - - +
228B TYR* 3.5 23.3 - - + -
15I LYS* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 5.6 0.2 - - - -
57A HIS* 3.0 15.4 + - - -
99B TYR* 3.9 0.8 + - - +
102B ASP* 3.2 30.4 + - - +
195B SER* 3.3 1.2 + - - -
212B ILE* 3.3 2.9 + - - -
213B THR* 1.3 76.1 - - - +
215B TRP* 1.3 76.5 + - - +
227B ILE* 3.6 15.8 + - - -
229B THR* 4.0 18.6 - - - -
14I CYS* 3.4 1.4 - - - -
15I LYS* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TYR* 3.2 46.6 + + + +
168B CYS 4.9 4.3 - - - -
174B ASP* 3.1 43.5 - - + -
175B LYS 3.8 17.9 - - - -
176B VAL 5.1 0.7 - - - -
180B MET* 4.3 3.8 - - - +
214B SER* 1.3 93.8 + - - +
216B GLY* 1.3 83.3 + - - +
226B SER* 3.7 3.6 - - - -
227B ILE* 2.9 74.2 + - + +
13I PRO* 3.2 25.4 - - + +
14I CYS* 3.8 11.2 - - - +
15I LYS* 3.9 8.0 - - - -
----------------------------------------------------------
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