Contacts of the strand formed by residues 257 - 263 (chain A) in PDB entry 1TFZ
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 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.5 11.8 - - - -
204A ASP* 3.6 21.1 - - - +
205A HIS* 3.5 12.3 - - + -
206A ALA 3.2 17.0 + - - +
229A PHE* 4.6 7.2 - - + -
248A VAL* 4.4 14.4 - - + -
249A LEU 3.5 2.5 - - - +
250A ALA* 3.5 25.4 - - + -
254A GLU* 3.3 27.8 - - + +
255A MET 4.4 2.5 - - - +
256A VAL* 1.3 76.1 - - - +
258A LEU* 1.3 60.5 + - - +
259A PRO* 3.2 10.6 - - + +
393A GLY* 5.2 0.4 - - - -
394A GLY* 4.2 15.7 - - - +
398A PHE* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.0 11.7 - - + -
121A VAL* 4.0 26.9 - - + -
160A LEU* 4.5 23.8 - - + -
161A TYR* 5.7 4.0 - - + +
166A LEU* 4.4 18.6 - - + -
206A ALA* 3.6 11.0 - - + +
220A VAL* 4.7 8.3 - - + -
226A PHE* 3.7 28.5 - - + -
247A ALA 4.4 0.2 - - - +
249A LEU* 2.9 36.4 + - + +
256A VAL* 4.3 9.2 - - + -
257A LEU* 1.3 78.4 - - - +
259A PRO* 1.3 65.9 - - - +
260A ILE* 4.0 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 4.7 1.6 + - - -
205A HIS* 4.1 11.7 - - + -
206A ALA 3.3 17.5 - - - +
207A VAL* 3.4 15.4 - - + -
208A GLY 3.0 21.8 + - - -
247A ALA 3.3 11.7 - - - +
248A VAL* 4.0 17.5 - - + -
257A LEU* 3.2 12.6 - - + +
258A LEU* 1.3 87.7 - - - +
260A ILE* 1.3 63.8 + - - +
398A PHE* 4.8 0.9 - - + -
551A 869 3.4 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 4.2 24.5 - - + -
208A GLY 3.3 10.3 - - - +
210A VAL* 3.5 34.3 - - + -
213A LEU* 3.3 17.1 - - + +
216A ALA* 4.1 28.7 - - + +
217A LEU* 4.5 11.7 - - + -
220A VAL* 4.4 11.0 - - + -
246A SER* 3.2 4.0 - - - -
247A ALA 2.9 32.9 + - - +
249A LEU* 4.9 2.2 - - + -
258A LEU* 4.1 9.0 - - + +
259A PRO* 1.3 81.4 - - - +
261A ASN* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.3 8.5 - - - +
208A GLY 3.0 4.2 + - - -
209A ASN* 3.1 22.9 - - - +
210A VAL* 2.9 31.4 + - - +
213A LEU* 4.4 1.3 - - - -
244A LEU* 4.4 12.0 - - + +
245A ASN 3.2 7.6 - - - +
246A SER* 2.7 32.8 + - - +
260A ILE* 1.3 75.0 + - - +
262A GLU* 1.3 60.4 + - - +
273A ILE* 4.2 13.5 - - + -
286A GLN* 3.3 19.6 + - - +
551A 869 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL 3.2 6.7 - - - +
211A PRO 4.0 4.4 - - - +
212A GLU* 3.6 6.4 - - - +
213A LEU* 2.7 52.1 + - + +
214A GLY 4.3 1.7 + - - -
244A LEU* 3.3 6.9 - - - +
245A ASN* 3.0 53.4 + - + +
261A ASN* 1.3 75.1 - - - +
263A PRO* 1.3 80.3 - - + +
273A ILE* 4.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL 3.2 14.6 - - - +
211A PRO* 3.8 11.5 - - + +
243A GLY 3.7 0.2 - - - +
262A GLU* 1.3 99.1 - - + +
264A VAL* 1.3 64.3 + - - +
265A HIS* 3.7 31.9 + - + +
271A SER* 3.3 26.9 - - - +
273A ILE* 3.8 9.2 - - + -
274A GLN* 3.8 20.0 - - + +
277A LEU* 4.0 9.9 - - + -
----------------------------------------------------------
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