Contacts of the strand formed by residues 192 - 199 (chain A) in PDB entry 3FUW
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 SER 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 5.1 2.5 - - - -
143A VAL 3.2 17.3 + - - -
144A GLN* 4.6 5.0 - - - +
145A LYS* 3.8 1.1 - - - +
178A ASP* 3.4 5.2 - - - +
179A LEU* 2.8 34.7 + - - -
184A PHE* 3.4 37.2 - - - -
188A PRO* 4.7 3.6 - - - +
190A VAL* 4.2 4.9 + - - +
191A TRP* 1.3 78.2 + - - +
193A SER* 1.3 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE 3.6 0.9 - - - +
142A LEU* 3.3 6.1 - - - -
143A VAL* 2.8 31.5 + - - +
145A LYS* 3.6 13.2 - - - +
148A ALA* 3.5 24.9 - - - -
175A ARG* 3.6 15.0 - - - -
177A PHE 3.2 11.2 - - - -
178A ASP* 2.7 20.9 + - - -
179A LEU* 4.2 5.4 - - - -
192A SER* 1.3 74.9 + - - +
194A LEU* 1.3 61.0 + - - +
195A VAL 3.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 3.8 37.7 - - + +
39A ILE* 3.8 20.0 - - + +
42A ALA* 4.1 8.7 - - + -
140A VAL* 3.6 28.5 - - + -
141A PHE 3.6 6.3 - - - +
142A LEU* 3.8 13.2 - - + -
175A ARG* 3.7 3.5 - - - +
176A LEU* 2.8 50.2 + - + +
177A PHE* 2.8 26.2 + - + +
179A LEU* 3.8 5.5 - - + +
193A SER* 1.3 69.6 - - - +
195A VAL* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU 3.7 0.9 - - - +
140A VAL* 3.3 6.6 - - - +
141A PHE* 2.9 54.3 + - + +
143A VAL* 3.7 14.6 - - + -
148A ALA* 3.6 35.4 - - + +
151A MET* 4.3 8.3 - - + -
152A THR* 5.2 2.7 - - + -
174A GLU 3.3 11.7 - - - +
175A ARG* 4.8 3.6 - - + -
193A SER* 4.2 0.9 - - - +
194A LEU* 1.3 81.0 - - - +
196A ARG* 1.3 63.0 - - - +
197A LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 4.7 2.0 + - - -
42A ALA* 2.9 42.1 + - - +
138A ARG* 3.9 19.0 - - + +
139A LEU 3.4 2.9 - - - -
140A VAL* 3.9 12.6 - - + -
172A VAL 3.8 0.7 - - - +
173A ALA* 3.5 2.3 - - - -
174A GLU* 2.8 77.0 + - + +
176A LEU* 3.8 30.2 - - + +
194A LEU 4.4 0.4 + - - -
195A VAL* 1.3 75.2 - - - +
197A LEU* 1.3 63.9 + - - +
198A THR* 4.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.7 29.8 - - + -
131A LEU* 4.1 18.4 - - + -
138A ARG* 3.4 6.1 - - - +
139A LEU* 2.8 46.2 + - + +
141A PHE* 3.7 20.0 - - + -
151A MET* 4.9 2.9 - - + -
167A VAL* 3.7 16.4 - - + -
171A ALA* 4.3 8.5 - - + -
172A VAL 3.3 2.9 - - - +
173A ALA* 3.4 31.2 - - + -
195A VAL* 3.6 14.1 - - + -
196A ARG* 1.3 75.3 - - - +
198A THR* 1.3 62.2 + - - +
199A PRO* 3.5 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.9 13.0 - - - +
138A ARG* 4.7 8.2 - - - +
171A ALA* 3.6 2.5 - - - -
172A VAL* 2.9 46.6 + - + +
174A GLU* 4.5 6.1 + - - -
196A ARG* 4.2 15.1 - - - +
197A LEU* 1.3 74.9 + - - +
199A PRO* 1.3 73.8 - - - +
200A THR* 3.5 4.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.4 12.6 - - + -
134A GLY* 5.8 7.2 - - - +
136A PHE* 3.1 24.5 - - + +
137A ALA 3.5 19.3 - - - +
139A LEU* 3.7 19.5 - - + -
170A HIS* 3.2 11.9 - - + +
171A ALA* 3.7 1.6 - - + -
197A LEU 3.5 11.0 - - - +
198A THR* 1.3 92.8 - - - +
200A THR* 1.3 61.5 + - - +
201A GLY 3.6 3.8 - - - +
----------------------------------------------------------
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