Contacts of the strand formed by residues 202 - 209 (chain A) in PDB entry 4YCG
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 LYS 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 5.7 3.0 - - - +
109A ILE* 4.0 19.5 - - + +
110A LEU 3.4 15.5 - - - +
111A ILE* 4.0 33.6 - - + +
112A PHE 4.7 0.2 - - - +
151A ASP* 3.3 11.3 - - - +
152A VAL* 3.4 28.3 + - + +
155A ASP* 2.9 28.7 + - + +
191A TRP* 3.2 16.8 - - - -
199A ASN* 5.4 4.0 - - - +
200A LYS* 3.8 16.2 - - - +
201A ASN* 1.3 79.3 - - - +
203A LEU* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A HIS 3.8 0.2 - - - +
109A ILE* 3.5 2.4 - - - -
110A LEU* 2.8 54.7 + - + -
112A PHE* 4.0 6.3 - - + -
127A LEU* 3.8 22.7 - - + -
149A VAL* 4.0 17.5 - - + -
150A TYR 3.1 19.7 - - - +
151A ASP* 4.2 3.4 - - - -
152A VAL* 3.7 8.1 - - - -
169A LEU* 4.4 9.4 - - + -
184A VAL* 4.7 3.1 - - + -
187A ALA* 4.9 0.7 - - + -
191A TRP* 3.7 12.8 - - + -
202A LYS* 1.3 78.9 - - - +
204A GLU* 1.3 56.1 + - - +
205A VAL* 4.2 2.0 - - + -
231A PHE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 5.2 0.4 - - - -
108A HIS 3.2 13.9 - - - +
109A ILE* 4.1 13.5 - - + +
149A VAL* 3.2 1.2 - - - -
150A TYR* 2.6 45.4 + - - +
152A VAL* 3.4 17.0 - - + +
160A ASP* 3.8 8.4 - - - +
161A GLN* 2.8 57.6 + - - +
166A LYS* 3.2 21.4 + - + +
203A LEU* 1.3 73.4 - - - +
205A VAL* 1.3 65.4 + - - +
206A THR* 3.7 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN 3.7 1.0 - - - +
107A LYS 3.7 0.7 - - - -
108A HIS* 2.6 43.9 + - + +
110A LEU* 4.0 22.0 - - + -
127A LEU* 4.1 9.2 - - + -
129A LEU* 3.9 13.0 - - + -
147A MET* 4.8 5.6 - - + -
148A VAL 3.3 9.2 - - - +
149A VAL* 3.8 24.0 - - + -
182A LEU* 5.5 0.4 - - + -
203A LEU* 4.2 2.0 - - + -
204A GLU* 1.3 75.1 - - - +
206A THR* 1.3 72.0 + - - +
207A VAL* 4.4 5.4 - - + -
219A ILE* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.9 28.5 - - + -
106A GLN 3.1 7.9 - - - +
107A LYS* 4.6 2.9 - - + -
147A MET* 3.1 6.1 - - - +
148A VAL* 2.7 55.0 + - - +
150A TYR* 3.7 9.8 + - + +
161A GLN* 3.7 14.6 - - + +
204A GLU* 3.7 24.0 - - - +
205A VAL* 1.3 77.4 - - - +
207A VAL* 1.3 61.7 + - - +
208A GLN* 4.1 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.2 5.3 - - - +
106A GLN* 2.8 43.8 + - + +
108A HIS* 4.3 6.3 - - + -
146A SER 3.7 7.2 - - - +
147A MET* 4.3 7.0 - - + -
174A ILE* 4.5 9.9 - - + -
205A VAL* 4.4 4.0 - - + -
206A THR* 1.3 76.7 - - - +
208A GLN* 1.3 62.3 + - - +
209A SER* 3.7 2.1 + - - -
217A LEU* 3.6 33.1 - - + +
218A ASP* 3.7 24.7 - - - +
219A ILE* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 2.7 39.0 + - - +
105A PHE* 3.2 20.9 - - + -
145A GLY* 3.4 3.5 - - - -
146A SER* 2.7 51.3 + - - +
147A MET* 5.7 0.2 - - - -
206A THR* 4.1 1.4 - - - -
207A VAL* 1.3 71.2 - - - +
209A SER* 1.3 84.6 + - - +
210A HIS* 3.6 9.4 - - + -
217A LEU* 4.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO 4.9 1.0 + - - -
105A PHE* 5.3 0.8 - - - +
207A VAL* 3.7 4.2 + - - +
208A GLN* 1.3 91.6 + - - +
210A HIS* 1.3 71.7 + - - +
213A SER* 4.0 4.0 - - - -
214A CYS 2.6 28.2 + - - -
215A ASP* 4.7 4.7 - - - -
217A LEU* 4.1 24.4 - - - +
----------------------------------------------------------
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