Contacts of the strand formed by residues 199 - 204 (chain B) in PDB entry 1S5H
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 THR 199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 3.4 8.5 - - - -
160B ASN* 2.8 39.8 + - - -
197B THR* 3.7 14.2 + - - +
198B VAL* 1.3 77.9 + - - +
200B CYS* 1.3 62.9 + - - +
201B ASN* 4.2 7.5 - - - +
212B ASP* 4.0 12.8 - - + -
213B LYS 3.2 35.2 - - - +
214B LYS* 3.6 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.7 19.3 - - - -
145B CYS* 3.1 42.4 - - - -
157B VAL* 4.5 2.5 - - + -
158B THR 3.3 6.3 - - - +
159B TRP* 3.4 26.1 - - + -
199B THR* 1.3 74.4 - - - +
201B ASN* 1.3 60.5 + - - +
202B VAL* 4.3 3.6 - - - -
211B VAL 3.9 0.7 - - - +
212B ASP* 3.4 3.3 - - - -
213B LYS* 3.0 38.0 + - - -
215B ILE* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR 3.3 5.7 - - - +
157B VAL* 3.3 2.4 - - - -
158B THR* 2.6 57.4 + - - +
160B ASN* 3.7 1.1 + - - +
161B SER* 2.7 40.1 + - - +
199B THR* 4.3 10.5 + - - +
200B CYS* 1.3 75.7 - - - +
202B VAL* 1.3 60.9 + - - +
203B ALA 4.1 0.2 - - - -
210B LYS* 4.5 17.7 - - + -
211B VAL 3.6 4.9 - - - +
212B ASP* 2.6 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124B PRO* 4.1 17.3 - - + +
126B VAL* 3.9 31.6 - - + -
147B VAL* 3.9 37.9 - - + -
155B VAL* 4.4 8.1 - - + -
156B THR 3.6 2.9 - - - +
157B VAL* 4.3 10.8 - - + -
200B CYS* 4.3 9.0 - - - -
201B ASN* 1.3 77.6 - - - +
203B ALA* 1.3 66.8 + - - +
204B HIS* 5.5 0.2 - - - +
209B THR* 3.8 1.4 + - - +
210B LYS* 3.1 4.9 - - - +
211B VAL* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.1 8.7 - - - +
156B THR* 3.0 46.1 + - - +
201B ASN 4.1 0.4 + - - -
202B VAL* 1.3 74.7 - - - +
204B HIS* 1.3 59.5 - - - +
205B PRO* 3.5 8.2 - - + +
209B THR 3.4 5.8 - - - +
210B LYS* 4.0 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.3 0.4 - - + -
122B THR 3.4 12.6 - - - -
123B PRO* 3.8 4.8 - - - +
124B PRO* 3.6 18.8 - - + -
150B TYR* 3.9 5.7 - + - -
151B PHE 3.3 22.8 + - - -
152B PRO 2.9 22.4 + - - -
154B PRO 3.3 19.5 - - - -
155B VAL* 3.6 13.0 - - + -
202B VAL 4.1 0.4 + - - -
203B ALA* 1.3 73.1 - - - +
205B PRO* 1.3 67.3 - - - +
206B ALA* 3.2 15.7 - - + +
207B SER* 2.7 39.6 + - - -
208B SER 3.2 7.1 + - - -
209B THR* 2.7 25.2 + - - +
----------------------------------------------------------
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