Contacts of the strand formed by residues 200 - 207 (chain A) in PDB entry 3T2E
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 TYR 200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 2.8 27.5 + - - -
170A VAL* 3.8 17.3 - - + -
171A LEU 3.5 2.9 - - - -
172A ASP* 3.7 33.0 + - + -
179A TYR* 3.9 16.9 + + - -
192A GLY 5.5 0.9 - - - -
193A LEU* 3.3 62.0 - - + +
194A ILE* 3.5 6.6 - - - -
196A THR* 3.0 16.5 + - + +
199A ARG* 1.3 113.1 + - + +
201A ILE* 1.3 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 3.9 12.3 - - + +
137A GLY* 4.0 8.1 - - - +
140A ASN* 3.6 7.0 - - - +
170A VAL* 3.5 4.1 - - - +
171A LEU* 2.9 33.2 + - - +
173A VAL* 3.8 35.2 - - + -
197A THR 3.4 26.9 - - - +
198A GLY* 4.1 4.5 - - - +
199A ARG 4.0 5.6 - - - -
200A TYR* 1.3 72.6 - - - +
202A ILE* 1.3 78.4 + - - +
203A ARG* 3.2 1.4 + - - +
217A ASN* 3.7 15.3 - - - +
219A VAL* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 2.9 26.2 + - - +
143A LEU* 3.7 34.3 - - + -
144A TYR 4.0 0.7 - - - +
168A PHE* 3.7 26.9 - - + -
169A GLU 3.8 5.4 - - - +
170A VAL* 4.4 5.4 - - + +
194A ILE* 3.8 36.3 - - + +
201A ILE* 1.3 72.7 - - - +
203A ARG* 1.4 61.2 + - - +
204A LYS 3.9 9.4 - - - +
205A VAL* 3.8 28.0 - - + -
217A ASN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 4.3 18.7 - - - +
169A GLU* 2.8 42.1 + - + +
171A LEU* 3.6 32.6 - - + +
176A HIS* 5.5 4.9 - - - -
178A VAL* 3.5 26.1 - - - +
201A ILE 3.2 4.1 + - - +
202A ILE* 1.4 75.6 - - - +
204A LYS* 1.3 78.8 + - + +
216A ALA* 3.4 0.5 - - - +
217A ASN* 2.8 33.3 + - - +
219A VAL* 3.6 36.0 + - + +
220A GLU* 5.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 3.1 23.6 + - - -
115A GLU 2.8 30.1 + - - +
116A MET* 4.5 4.2 - - - +
168A PHE* 3.8 0.2 - - - -
169A GLU* 2.9 54.4 + - - +
202A ILE* 3.9 2.0 - - - +
203A ARG* 1.3 93.6 - - + +
205A VAL* 1.3 69.1 + - - +
206A PHE* 3.6 29.4 - - + -
215A ALA 3.3 12.1 - - - +
216A ALA* 4.0 7.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
143A LEU* 4.7 3.1 - - + -
147A PHE* 3.8 48.2 - - + -
166A PHE* 3.9 21.8 - - + -
167A ILE 3.2 12.3 - - - +
168A PHE* 4.1 11.9 - - + -
202A ILE* 3.8 20.4 - - + -
204A LYS* 1.3 78.0 - - - +
206A PHE* 1.3 64.1 + - - +
213A PRO* 3.8 1.4 - - - +
214A ALA* 2.8 28.3 + - + -
215A ALA* 3.0 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.4 9.4 - - - -
167A ILE* 2.8 60.8 + - + -
169A GLU* 3.7 18.8 - - + -
180A LEU* 5.5 2.9 - - + -
204A LYS* 3.6 40.8 - - + -
205A VAL* 1.3 75.4 - - - +
207A ARG* 1.3 63.7 + - - +
211A GLY* 3.5 23.1 - - - +
212A ALA 3.2 6.3 - - - +
213A PRO* 3.7 24.7 - - + -
214A ALA* 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.1 32.9 + - - -
162A MET* 5.7 0.2 - - - +
165A GLY 4.7 2.0 - - - +
166A PHE* 3.7 21.5 - - + -
167A ILE* 4.2 2.5 - - - +
206A PHE* 1.3 72.3 - - - +
208A ARG* 1.3 58.2 + - - +
209A ALA* 3.8 21.9 - - + +
210A ASP* 3.4 32.3 + - - +
211A GLY* 2.7 33.1 + - - -
212A ALA* 2.8 17.5 + - + +
214A ALA* 4.5 0.8 - - - +
243A SER 4.0 11.7 + - - -
244A GLY* 3.6 30.2 + - - +
245A LEU* 4.0 15.0 - - + +
----------------------------------------------------------
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