Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 3PE7
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 ASP 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 3.1 51.4 + - + +
197A PRO 3.1 0.9 - - - +
198A TYR* 1.3 81.3 - - - +
200A ASP* 1.3 64.8 + - - +
201A SER* 3.1 20.8 + - - -
202A THR* 2.6 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN* 3.0 37.3 + - - +
134A SER* 4.5 4.2 + - - -
135A ASP* 4.9 7.2 + - - +
138A LYS* 3.0 31.0 + - - +
195A TYR* 3.3 16.7 - - + -
196A ARG 4.8 1.6 - - - +
198A TYR* 4.1 2.8 + - - -
199A ASP* 1.3 74.7 + - - +
201A SER* 1.3 60.5 + - - +
202A THR 3.2 2.2 + - - -
223A GLU* 3.2 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.0 15.6 + - - -
200A ASP* 1.3 78.3 - - - +
202A THR* 1.3 58.8 + - - +
222A ASN* 3.1 19.2 - - - +
223A GLU* 3.1 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 3.9 2.1 - - - -
196A ARG* 2.9 36.4 + - - -
199A ASP* 2.6 29.7 + - - +
201A SER* 1.3 79.5 + - - +
203A VAL* 1.3 68.4 + - - +
220A LEU* 4.0 34.5 - - + -
221A ILE 3.8 2.2 - - - +
222A ASN* 5.2 0.9 + - - -
229A ARG* 4.5 13.0 + - - +
245A TRP* 4.1 15.5 - - + -
271A PRO* 5.1 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 4.3 21.5 - - + -
170A LEU* 4.5 13.2 - - + -
183A ILE* 4.5 5.2 - - + -
193A PRO* 4.4 7.0 - - + -
194A ILE 3.7 14.8 - - - +
195A TYR* 4.0 25.8 - - + -
200A ASP 4.6 0.2 - - - +
202A THR* 1.3 77.9 - - - +
204A ALA* 1.3 74.4 + - - +
205A PHE* 4.1 0.2 - - - -
220A LEU* 3.3 5.4 - - - -
221A ILE* 2.8 53.0 + - + +
223A GLU* 4.5 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO* 3.2 3.3 - - - +
194A ILE* 2.8 44.5 + - + -
202A THR 4.2 0.4 - - - -
203A VAL* 1.3 76.2 - - - +
205A PHE* 1.3 61.8 + - - +
219A TRP 3.3 8.5 - - - +
220A LEU* 3.7 9.8 - - + +
243A GLU* 6.0 2.0 - - + -
245A TRP* 3.7 33.0 - - + +
252A LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 5.7 1.1 - - + -
170A LEU* 3.9 23.3 - - + -
184A LEU* 3.6 26.2 - - + -
190A LEU* 3.9 20.6 - - + -
191A GLY 3.6 8.5 - - - +
192A HIS 3.6 11.0 - - - -
193A PRO* 4.0 8.1 - - + -
203A VAL 4.1 0.9 - - - -
204A ALA* 1.3 78.2 - - - +
206A CYS* 1.3 71.9 + - - +
207A HIS* 4.3 5.4 - + - -
218A MET* 3.9 1.7 - - - +
219A TRP* 3.0 63.4 + + + +
220A LEU 4.1 3.6 - - - -
221A ILE* 3.8 30.5 - - + -
228A MET* 4.0 13.5 - - + -
243A GLU* 5.3 3.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
190A LEU* 3.4 6.1 - - - -
191A GLY* 2.8 55.5 + - - -
192A HIS* 4.0 7.5 + - - -
205A PHE* 1.3 81.1 - - - +
207A HIS* 1.3 67.0 + - - +
208A GLU* 4.0 11.7 - - - -
217A ARG* 3.1 51.4 - - - +
218A MET* 5.1 0.2 - - - -
219A TRP* 4.6 0.2 - - - -
243A GLU* 3.8 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR* 6.1 1.1 - - + -
186A GLU* 4.2 2.6 + - - -
188A GLN* 3.4 38.3 + - - +
189A TRP 3.5 5.8 - - - +
190A LEU* 3.7 22.5 - - + +
205A PHE* 4.3 5.0 - + - -
206A CYS* 1.3 72.3 - - - +
208A GLU* 1.3 65.1 + - - +
209A GLY 3.9 0.3 + - - +
214A VAL* 3.6 19.2 - - + +
215A ASP* 2.7 26.7 + - - +
216A ALA 3.4 10.3 - - - +
217A ARG* 3.0 22.2 + - - +
219A TRP* 3.3 48.1 + + - -
228A MET* 5.7 1.4 - - - -
----------------------------------------------------------
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