Contacts of the strand formed by residues 198 - 207 (chain B) in PDB entry 5IPL
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 LEU 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.4 15.7 - - + -
30B PRO* 3.8 19.1 - - + -
31B LEU 3.5 13.0 - - - +
32B GLU* 4.1 13.7 - - + -
33B ARG 4.8 0.2 - - - +
189B ALA* 3.5 9.2 - - - +
190B ALA* 2.9 34.7 + - + +
192B VAL* 3.3 30.5 - - + -
195B ARG* 3.5 51.6 - - + +
196B THR 3.2 1.8 - - - +
197B ASP* 1.3 84.0 - - - +
199B ASP* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO 3.9 0.9 - - - -
31B LEU* 2.8 50.5 + - - +
32B GLU 3.2 12.9 - - - +
33B ARG* 4.6 2.2 - - - -
34B GLY* 3.9 10.8 + - - -
36B GLY* 3.5 18.6 + - - -
37B HIS* 4.8 1.2 + - - -
187B VAL* 3.3 26.8 - - + +
188B GLU 3.3 14.6 - - - +
189B ALA* 4.4 1.1 - - - -
190B ALA* 3.7 7.2 - - - +
197B ASP 4.9 1.3 - - - +
198B LEU* 1.3 75.8 - - - +
200B LYS* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 5.3 7.4 - - + -
28B LEU 3.4 13.5 - - - +
29B GLU* 3.6 33.4 + - + +
31B LEU* 4.3 0.4 - - - -
186B ASN 3.6 0.7 - - - +
187B VAL* 3.4 7.1 - - - -
188B GLU* 2.8 56.2 + - + +
189B ALA 3.8 20.0 + - - -
190B ALA* 3.9 6.0 - - + +
199B ASP* 1.3 74.8 - - - +
201B LEU* 1.3 60.0 + - - +
202B VAL* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 5.6 4.7 - - + -
26B VAL 3.4 2.9 - - - +
27B THR* 3.4 0.2 - - - -
28B LEU* 3.0 44.2 + - + +
31B LEU* 3.3 24.4 - - + +
36B GLY* 3.4 26.0 - - - +
39B LEU* 4.6 9.0 - - + -
40B GLY* 4.0 10.3 - - - +
43B LEU* 5.0 3.4 - - + -
185B TYR* 3.5 32.1 - - + -
186B ASN 3.6 2.0 - - - +
187B VAL* 3.7 10.1 - - + +
200B LYS* 1.3 73.6 - - - +
202B VAL* 1.3 59.3 + - - +
203B ILE* 3.8 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.8 7.9 - - + -
26B VAL 3.4 9.4 - - - +
27B THR* 4.0 23.6 - - + -
184B ALA 3.9 0.3 - - - +
185B TYR* 3.3 2.1 - - - -
186B ASN* 2.9 53.5 + - + +
188B GLU* 3.7 19.3 - - - +
200B LYS* 4.4 13.9 - - + -
201B LEU* 1.3 76.5 - - - +
203B ILE* 1.3 63.1 + - - +
204B GLU* 3.7 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 3.5 4.7 - - - +
26B VAL* 2.9 46.6 + - + +
28B LEU* 6.2 0.9 - - + -
40B GLY* 4.9 4.0 - - - +
43B LEU* 4.2 24.2 - - + -
47B LEU* 5.3 2.7 - - + -
183B ILE* 4.0 27.8 - - + -
184B ALA 3.6 6.3 - - - +
185B TYR* 4.0 11.9 - - + -
201B LEU* 3.8 32.8 - - + -
202B VAL* 1.3 74.4 - - - +
204B GLU* 1.3 65.9 + - - +
205B MET* 3.8 11.3 + - + +
217B ILE* 5.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.7 21.8 + - + -
24B ALA 3.5 3.4 - - - +
25B LYS* 3.7 41.5 + - + +
182B ARG* 4.1 14.1 + - - +
183B ILE* 3.5 3.8 - - - +
184B ALA* 2.8 42.0 + - + +
186B ASN* 3.7 23.0 + - - +
202B VAL* 3.7 5.7 + - + +
203B ILE* 1.3 75.7 - - - +
205B MET* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR 3.7 0.7 - - - +
23B HIS* 3.4 8.2 + - - -
24B ALA* 3.0 35.6 + - + +
26B VAL* 6.5 0.7 - - + -
47B LEU* 3.9 30.1 - - + -
180B VAL* 4.8 8.3 - - + -
182B ARG* 3.6 7.9 - - - +
183B ILE* 4.4 8.1 - - + +
203B ILE* 3.8 6.7 + - + +
204B GLU* 1.3 75.2 - - - +
206B GLU* 1.3 71.5 + - - +
207B THR* 4.3 10.3 - - + +
213B PRO* 3.5 36.8 - - + +
216B ALA* 4.6 7.4 - - - -
217B ILE* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.4 24.8 + - - +
23B HIS* 4.1 18.9 - - + +
180B VAL* 3.8 1.2 - - - +
181B GLU* 2.8 34.4 + - + +
182B ARG* 2.9 57.9 + - + +
205B MET* 1.3 75.5 - - - +
207B THR* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 4.4 1.6 - - - +
22B THR* 2.4 47.5 + - - +
179B PRO* 2.9 21.8 + - - +
180B VAL* 4.2 7.9 - - - +
181B GLU* 3.9 4.9 - - - +
205B MET* 4.5 8.1 - - + -
206B GLU* 1.3 74.6 - - - +
208B ASN* 1.3 70.9 + - - +
211B ILE* 3.4 29.1 + - - +
212B ASP 4.4 0.4 - - - -
213B PRO* 3.5 33.2 - - + -
----------------------------------------------------------
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