Contacts of the strand formed by residues 202 - 210 (chain A) in PDB entry 2YD4
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 GLY 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 4.6 1.1 - - - -
170A ASP* 3.4 14.6 - - - -
200A ASP 3.5 2.2 + - - -
201A GLN* 1.3 77.4 - - - +
203A LYS* 1.3 58.1 + - - -
204A TYR* 3.6 12.1 - - - -
221A ASN* 3.4 2.9 - - - -
222A LEU 3.0 28.6 + - - -
1234A PEG 3.7 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 5.5 0.2 - - - +
168A PHE 3.8 0.9 - - - +
169A LYS* 3.3 2.3 - - - +
170A ASP* 2.8 44.1 + - - +
171A PHE* 3.9 35.5 + - + -
202A GLY* 1.3 70.3 - - - -
204A TYR* 1.3 61.8 + - - +
205A GLU* 5.0 7.6 - - - +
219A PRO* 3.7 31.1 - - + +
220A ALA 3.8 0.4 - - - +
221A ASN* 3.5 23.5 + - - +
1234A PEG 4.0 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 4.8 1.3 - - - +
153A MET* 3.7 31.2 - - + -
167A TRP* 4.2 11.4 - + + -
168A PHE 3.3 7.4 - - - +
169A LYS* 3.7 33.7 + - + +
174A VAL* 4.8 2.2 - - + -
183A ILE* 5.7 4.6 - - + +
191A LEU* 3.7 26.2 - - + -
193A ILE* 3.7 14.4 - - + +
200A ASP* 2.7 35.6 + - - +
202A GLY* 3.6 17.0 - - - -
203A LYS* 1.3 74.8 - - - +
205A GLU* 1.3 61.0 + - - +
218A SER 4.4 0.5 - - - +
219A PRO* 3.3 5.0 - - - +
220A ALA* 2.8 47.9 + - + +
222A LEU* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.3 4.2 - - - +
91A ARG* 2.8 44.8 + - - -
93A GLN* 4.6 2.4 + - - -
140A PRO* 5.2 0.2 - - - -
167A TRP* 3.3 10.9 - - - -
168A PHE* 2.9 47.4 + - + +
171A PHE* 4.1 9.1 + - - -
203A LYS* 5.0 6.9 - - + +
204A TYR* 1.3 78.2 - - - +
206A CYS* 1.3 60.3 + - - +
207A VAL* 4.5 0.5 - - - +
216A TYR* 4.0 24.3 - - + -
217A SER* 3.9 13.7 - - - +
219A PRO* 4.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.2 7.9 - - - -
140A PRO* 4.2 1.3 - - + -
155A CYS* 2.0 54.7 - - + -
165A ILE* 3.9 18.8 - - - -
166A THR 3.6 4.0 - - - -
167A TRP* 3.9 14.8 - - + -
205A GLU* 1.3 73.8 - - - +
207A VAL* 1.3 68.0 + - - +
216A TYR* 3.4 4.0 - - - +
217A SER* 2.8 41.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
164A GLU 3.4 1.7 - - - +
165A ILE* 3.3 6.6 - - - +
166A THR* 2.7 49.1 + - - +
168A PHE* 3.7 21.3 - - + -
205A GLU 4.5 1.8 - - - +
206A CYS* 1.3 82.9 - - - +
208A ALA* 1.3 58.8 + - - +
209A SER* 3.7 8.1 - - - +
214A VAL* 3.3 33.4 - - + -
215A ARG 3.5 3.8 - - - +
216A TYR* 3.5 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PRO* 3.5 21.7 - - + +
135A ASN 4.9 0.2 - - - -
136A ILE* 3.7 13.8 - - + +
157A ALA* 3.6 31.9 - - + -
163A PRO* 4.0 4.9 - - + -
164A GLU 3.5 4.5 - - - -
165A ILE* 3.9 5.2 - - + -
207A VAL* 1.3 71.6 - - - +
209A SER* 1.3 62.0 + - - +
214A VAL* 3.4 2.8 - - - +
215A ARG 2.9 33.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
41A GLN* 5.3 2.4 + - - -
134A PRO* 4.3 0.2 - - - -
163A PRO* 3.2 4.9 - - - +
164A GLU* 2.8 48.4 + - - +
166A THR* 5.0 3.4 + - - -
207A VAL* 3.7 8.5 + - - +
208A ALA* 1.3 76.8 - - - +
210A ASN* 1.3 61.8 + - - +
213A GLY 3.5 6.1 - - - -
214A VAL* 3.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 3.0 25.1 + - - -
134A PRO* 3.3 14.5 - - - +
159A GLY* 4.1 2.4 - - - -
160A ASN 3.6 6.7 + - - +
161A PRO* 2.9 38.0 + - + +
162A ASP 4.6 1.3 - - - +
163A PRO* 4.1 5.3 - - + +
164A GLU* 4.8 4.7 - - - +
209A SER* 1.3 77.7 - - - +
211A SER* 1.3 64.1 + - - +
212A ALA* 2.9 22.5 + - - +
213A GLY* 3.0 24.2 + - - +
----------------------------------------------------------
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