Contacts of the strand formed by residues 199 - 206 (chain B) in PDB entry 6CU0
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 PHE 199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.5 30.4 + + - +
142B TYR* 3.8 4.3 - - - -
144B PHE* 3.6 31.9 - + + -
145B PHE 3.5 9.2 - - - -
146B GLN* 4.1 13.5 - - + -
181B LEU* 3.8 7.2 - - - +
198B GLY* 1.3 74.4 - - - +
200B GLN* 1.3 74.1 + - - +
142D TYR* 3.1 21.1 - - - -
199D PHE* 3.3 46.6 + + + +
200D GLN* 4.6 3.4 - - + +
201D GLY 3.2 33.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLN* 3.3 38.9 + - + +
148A GLU* 6.2 0.2 - - - +
197A PHE* 3.7 22.3 - - - +
198A GLY 5.7 1.2 + - - +
199A PHE* 4.7 7.0 - - + +
144B PHE* 3.1 3.8 - - - +
145B PHE* 2.8 40.0 + - + +
179B LEU* 3.7 15.8 - - + +
180B ALA 2.9 35.5 + - - +
181B LEU* 4.0 13.5 - - + +
199B PHE* 1.3 84.5 + - - +
201B GLY* 1.3 61.0 + - - +
202B ARG* 4.3 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 4.1 1.6 - - - -
146A GLN* 2.9 17.0 - - - +
199A PHE* 3.1 18.2 - - - -
142B TYR* 3.9 14.1 - - - -
143B VAL 3.1 13.5 - - - -
144B PHE* 3.7 8.5 - - - -
179B LEU* 4.1 2.2 - - - -
199B PHE* 3.8 5.3 - - - -
200B GLN* 1.3 78.5 - - - +
202B ARG* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 3.7 20.4 - - - +
96A VAL* 5.3 3.8 - - - +
117A GLY* 5.3 5.9 - - - -
144A PHE* 3.9 13.9 - - + -
146A GLN* 3.0 31.1 - - - +
231A GLY 3.2 26.3 + - - -
232A ALA* 4.5 6.1 + - - +
234A VAL* 3.5 14.2 - - + +
142B TYR* 3.9 9.1 - - - -
143B VAL* 2.9 30.0 + - - +
177B ALA 5.7 0.8 + - - -
178B ALA 3.9 17.4 + - - -
179B LEU* 3.4 25.9 - - + +
200B GLN* 4.3 6.9 + - - -
201B GLY* 1.3 74.3 - - - +
203B LEU* 1.3 68.7 + - - +
204B LEU* 3.6 11.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 4.4 11.7 - - + -
93A ALA 3.4 26.5 - - - +
94A GLN* 2.9 45.7 + - + +
117A GLY* 5.0 0.5 - - - +
119A SER* 5.2 3.9 + - - +
144A PHE* 3.9 14.6 - - + -
237A LEU 3.9 11.2 - - - +
238A PHE* 3.8 22.9 - - + -
140B VAL* 4.0 14.8 - - + -
141B TYR 3.2 11.0 - - - +
142B TYR* 4.0 14.4 - - + +
202B ARG* 1.3 71.6 - - - +
204B LEU* 1.3 65.8 + - - +
205B HIS 4.3 0.2 - - - -
240B VAL* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 5.6 0.2 - - - +
140B VAL* 4.3 2.9 - - - -
141B TYR 2.8 30.7 + - - -
143B VAL* 3.7 28.3 - - + -
165B LEU* 3.7 26.7 - - + -
167B LEU* 4.9 4.5 - - + -
178B ALA* 3.9 33.0 - - + +
179B LEU* 5.2 1.8 - - + -
202B ARG* 4.1 15.9 - - + +
203B LEU* 1.3 83.0 - - - +
205B HIS* 1.3 63.5 + - - +
206B LEU* 3.3 25.8 + - + +
212B LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 6.2 2.5 - - - +
138B ALA* 5.4 2.9 - - + -
139B GLY* 3.4 20.2 + - - -
140B VAL* 4.0 17.7 - - + +
167B LEU* 5.2 4.5 - - - +
204B LEU* 1.3 70.8 - - - +
206B LEU* 1.3 79.7 + - - +
207B SER* 4.3 8.0 + - - -
210B GLN* 4.9 2.9 + - - -
39G ASN* 3.6 26.3 + - + -
60G ARG* 4.8 12.7 - - + +
61G THR* 6.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.9 26.0 - - + -
138B ALA* 3.5 2.4 - - - +
139B GLY 2.8 36.3 + - - +
141B TYR* 3.5 33.7 - - + -
143B VAL* 4.6 2.0 - - + -
167B LEU* 4.2 27.4 - - + -
204B LEU* 3.8 25.8 - - + +
205B HIS* 1.3 86.0 + - - +
207B SER* 1.3 67.0 + - - +
210B GLN* 4.4 8.1 - - + +
212B LEU* 4.2 12.1 - - + -
237B LEU* 4.4 9.4 - - + -
----------------------------------------------------------
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