Contacts of the strand formed by residues 303 - 308 (chain A) in PDB entry 2LTZ
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 TRP 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.6 17.0 - - + +
300A PRO* 2.8 50.1 + - + +
301A PRO* 4.4 3.5 - - - +
302A GLY* 1.3 85.3 - - - +
304A GLU* 1.3 72.0 + - - +
305A ILE 4.3 0.2 - - - -
315A PHE* 3.2 45.8 - + + -
316A VAL 4.6 0.9 - - - -
317A ASP* 3.1 28.7 - - + +
319A ASN* 5.2 4.3 - - - +
324A GLN* 3.9 21.1 - - + -
326A THR 4.9 2.7 - - - -
328A PRO* 4.3 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.7 4.7 - - - +
301A PRO 5.7 2.1 - - - +
302A GLY 4.9 2.0 - - - +
303A TRP* 1.3 85.1 - - - +
305A ILE* 1.3 59.8 + - - +
306A ARG* 4.1 0.4 + - - -
315A PHE* 3.0 7.3 - - - -
316A VAL* 2.8 63.5 + - + +
318A HIS* 2.6 43.9 + - + +
213B ARG 4.8 1.6 - - - +
214B TYR* 2.7 33.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.4 35.8 - - + +
304A GLU* 1.3 75.9 + - - +
306A ARG* 1.3 77.6 + - - +
307A ASN* 6.2 0.2 - - + -
313A VAL* 4.4 8.7 - - + -
315A PHE* 3.7 35.2 - - + -
329A ARG* 5.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU 4.1 0.9 + - - -
305A ILE* 1.3 86.1 - - - +
307A ASN* 1.3 65.0 + - - +
313A VAL* 3.5 6.0 - - - +
314A TYR* 2.8 78.4 + - + +
316A VAL* 5.9 2.4 - - + +
213B ARG 5.6 0.7 - - - +
214B TYR* 4.4 13.0 - - + +
215B PRO* 2.8 44.1 + - + -
216B MET* 4.7 3.6 - - - +
217B ASP* 2.6 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ARG* 1.3 80.2 + - - +
308A THR* 1.3 89.7 + - - +
309A ALA 4.0 0.2 + - - -
311A GLY* 3.8 4.7 - - - -
312A ARG 2.9 19.5 + - - +
313A VAL* 3.4 27.0 - - + +
314A TYR* 3.5 3.4 - - - -
329A ARG* 5.7 0.6 - - - +
217B ASP* 2.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASN* 1.3 86.2 + - - +
309A ALA* 1.3 51.8 + - - +
310A THR* 3.0 10.0 + - - -
311A GLY* 2.7 25.6 + - - -
312A ARG* 2.7 49.0 + - - +
314A TYR* 3.2 28.2 - - + -
325A PHE* 3.7 2.2 - - + -
209B PRO* 3.9 18.8 - - + -
217B ASP* 3.1 23.8 - - + +
----------------------------------------------------------
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