Contacts of the strand formed by residues 193 - 199 (chain D) in PDB entry 4QGC
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 193 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LYS* 3.4 4.2 - - - +
142D ILE* 2.8 54.5 + - + +
164D ILE* 4.0 29.6 - - + -
165D CYS* 3.8 16.2 - - + -
168D VAL* 3.8 22.4 - - + -
174D ILE* 4.5 5.8 - - + -
185D VAL* 4.0 18.4 - - + -
187D GLN 3.3 3.4 - - - +
188D LYS* 3.7 31.0 - - + -
192D PHE* 1.3 86.5 - - - +
194D VAL* 1.3 65.3 + - - +
195D THR* 4.0 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 5.5 7.9 - - + -
140D LEU 4.0 2.9 - - - +
141D LYS* 4.1 20.9 - - + +
185D VAL* 3.6 1.5 - - - -
186D LYS* 2.6 40.0 + - + +
187D GLN* 2.9 52.8 + - + +
192D PHE* 4.7 12.3 - - + -
193D LEU* 1.3 75.4 - - - +
195D THR* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 3.3 9.4 - - - +
140D LEU* 2.4 55.8 + - - +
142D ILE* 3.6 19.4 - - + +
174D ILE* 4.8 2.9 - - + -
183D LEU* 3.7 22.0 - - + -
184D GLN 3.4 36.6 - - - +
185D VAL* 3.5 15.5 - - + +
186D LYS* 4.5 2.9 - - - -
193D LEU* 4.0 5.2 + - + +
194D VAL* 1.3 76.7 - - - +
196D GLU* 1.3 56.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLY* 3.8 25.5 - - - +
138D ALA 3.8 3.1 - - - +
139D THR* 4.4 6.3 - - + +
183D LEU* 3.5 2.0 - - - -
184D GLN* 3.1 41.0 + - + +
186D LYS* 3.1 32.1 + - + +
195D THR* 1.3 74.8 - - - +
197D VAL* 1.3 68.0 + - - +
198D GLU* 3.3 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.1 22.0 - - + -
135D LYS 3.8 12.1 - - - +
136D LYS* 3.8 0.3 - - - -
137D GLY* 3.2 21.5 + - - -
138D ALA* 2.9 26.3 + - + +
139D THR 4.4 2.0 - - - +
140D LEU* 4.2 14.4 - - + -
181D ILE* 4.1 4.7 - - + -
183D LEU* 3.7 25.8 - - + -
196D GLU* 1.3 72.7 - - - +
198D GLU* 1.3 65.2 + - - +
199D ASN 3.9 2.0 - - - -
200D GLY* 3.8 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 4.6 11.3 + - - -
136D LYS* 3.7 19.2 + - - +
173D LYS* 3.3 30.7 + - - +
175D TYR* 5.2 3.7 + - - -
182D SER* 2.9 33.1 + - - +
183D LEU 4.2 4.0 - - - +
184D GLN* 4.5 9.0 - - + +
196D GLU* 3.3 6.7 + - - +
197D VAL* 1.3 73.5 - - - +
199D ASN* 1.3 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 4.9 9.5 + - - -
136D LYS* 3.7 23.8 - - + -
180D LEU 3.1 20.6 + - - -
181D ILE* 3.4 18.2 - - - +
182D SER* 2.3 29.2 + - - -
197D VAL* 3.9 2.9 - - - -
198D GLU* 1.3 93.9 - - + +
200D GLY* 1.3 61.7 + - - +
----------------------------------------------------------
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