Contacts of the strand formed by residues 194 - 201 (chain A) in PDB entry 5WWT
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 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A HIS* 3.7 34.3 - - + -
130A VAL 4.0 2.9 - - - +
131A TYR* 3.9 19.3 - - + +
132A ALA 4.5 0.7 - - - -
178A GLU* 3.5 45.0 - - + +
179A LEU* 3.7 19.4 - - - +
193A GLY* 1.3 72.4 - - - -
195A GLY* 1.3 62.4 + - - +
196A ILE 3.8 12.6 - - - +
197A ARG* 3.6 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL 2.9 13.3 + - - -
131A TYR* 4.0 0.8 - - - +
132A ALA 4.3 3.4 - - - -
135A ILE* 4.3 13.0 - - - +
177A SER* 3.5 5.0 + - - -
178A GLU* 2.9 26.2 + - - -
179A LEU* 3.9 17.2 + - - +
193A GLY 3.7 3.0 + - - -
194A MET* 1.3 74.6 - - - +
196A ILE* 1.3 70.1 + - - +
197A ARG 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 3.8 17.3 - - + -
116A VAL* 5.0 0.7 - - + -
129A HIS* 3.8 0.3 - - - +
130A VAL* 2.8 56.1 + - + +
135A ILE* 3.8 15.5 - - + -
142A MET* 5.7 0.9 - - + -
148A ILE* 3.6 33.4 - - + -
150A VAL* 3.7 29.2 - - + -
175A GLY* 3.9 22.2 - - - -
176A ILE 3.5 2.9 - - - +
177A SER* 4.8 1.8 - - - +
194A MET* 3.8 4.7 - - - +
195A GLY* 1.3 82.2 - - - +
197A ARG* 1.3 60.3 + - - +
198A MET* 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A HIS* 3.6 29.6 + - + +
175A GLY* 3.9 1.1 - - - -
176A ILE* 2.8 52.1 + - + +
178A GLU* 3.2 26.5 + - - +
194A MET* 3.6 28.1 - - + +
195A GLY 4.2 0.6 - - - -
196A ILE* 1.3 69.8 - - - +
198A MET* 1.3 65.6 + - - +
199A THR* 3.2 5.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.9 20.6 - - + -
128A ALA 3.8 21.5 - - - +
129A HIS* 3.1 32.0 + - + +
130A VAL* 4.1 12.1 - - - +
150A VAL* 3.7 24.5 - - + -
172A LEU 4.3 4.5 - - - +
173A GLY* 3.8 27.4 - - - +
174A ASN 3.8 16.8 - - - +
196A ILE* 3.3 6.5 + - - +
197A ARG* 1.3 70.5 - - - +
199A THR* 1.3 61.1 + - - +
201A PRO* 4.5 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.1 0.9 + - - -
147A VAL* 5.5 3.5 - - - +
174A ASN* 3.0 12.7 + - - +
175A GLY* 3.7 5.7 + - - -
176A ILE* 4.0 25.7 - - + +
197A ARG* 3.2 18.1 + - + +
198A MET* 1.3 75.0 - - - +
200A GLU* 1.3 73.1 + - - +
201A PRO* 3.7 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 4.3 6.1 - - - +
107A ILE* 4.1 25.7 - - + +
108A LYS 5.5 1.0 + - - -
173A GLY* 3.2 5.0 - - - -
174A ASN* 2.9 50.7 + - + +
199A THR* 1.3 89.4 + - - +
201A PRO* 1.3 64.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 3.0 37.7 + - - +
107A ILE* 4.5 2.2 - - - +
124A VAL* 5.1 9.2 - - + +
127A GLY* 6.4 0.9 - - - -
172A LEU 3.6 9.9 - - - +
173A GLY* 4.2 1.3 - - - -
198A MET* 4.5 21.3 - - + +
199A THR* 3.7 9.0 - - - +
200A GLU* 1.3 89.8 - - - +
202A VAL* 1.3 63.5 + - - +
203A TYR 3.4 21.8 - - - +
204A LEU* 4.0 18.8 - - + -
205A SER 5.1 0.9 - - - +
----------------------------------------------------------
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