Contacts of the strand formed by residues 317 - 322 (chain B) in PDB entry 1MS4
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 317 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 4.1 13.9 - - + -
304B HIS* 4.2 0.9 - - - +
305B PRO* 3.8 15.0 - - + -
315B ASP 3.7 0.4 - - - -
316B ARG* 1.3 73.4 - - - +
318B ASN* 1.3 60.5 + - - +
332B GLN* 3.3 5.2 - - - +
333B VAL* 2.8 43.5 + - + -
334B SER* 3.0 11.9 + - - -
340B SER* 3.2 18.3 + - - +
341B ALA 3.9 15.5 - - - +
343B SER* 3.5 28.3 - - - +
354B CYS* 4.3 3.4 - - - -
356B HIS* 3.6 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 3.2 8.4 - - - -
304B HIS 2.9 44.8 + - - +
306B LEU* 3.8 26.4 - - + +
316B ARG 3.0 5.7 + - - +
317B LEU* 1.3 75.0 - - - +
319B LEU* 1.3 70.2 + - - +
320B TRP* 3.5 26.8 - - - +
329B ASN* 2.3 35.3 + - - +
331B GLY* 3.3 17.6 + - - -
332B GLN* 3.5 6.8 + - - +
333B VAL* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 4.4 17.5 - - + -
302B PHE 3.6 4.5 - - - +
303B THR* 3.7 20.0 - - + -
318B ASN* 1.3 75.8 + - - +
320B TRP* 1.3 69.1 + - - +
330B VAL* 2.8 57.3 + - + -
331B GLY 2.7 15.4 + - - +
333B VAL* 3.6 19.9 - - + +
345B VAL* 4.5 9.2 - - + -
352B LEU* 4.4 9.4 - - + -
371B LEU* 4.5 3.4 - - + -
374B GLU* 4.1 19.5 - - + -
378B ILE* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TRP* 3.4 34.3 - - + +
300B MET 4.7 0.2 - - - -
301B LEU* 3.6 6.1 - - - +
302B PHE* 2.9 55.1 + + + +
304B HIS* 4.8 4.2 + - - +
306B LEU* 5.0 2.6 - - + +
318B ASN* 3.5 35.6 + - + +
319B LEU* 1.3 81.1 - - - +
321B LEU* 1.3 61.7 + - - +
322B THR* 5.8 1.1 - - + -
327B ILE* 3.9 12.3 - - + -
328B TYR 3.2 23.1 - - - -
329B ASN* 3.7 26.2 - - + -
330B VAL* 4.1 2.7 - - - -
472B ASN* 3.1 45.3 - - + -
474B ARG* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 3.8 29.6 - - + -
300B MET 3.6 11.0 - - - +
301B LEU* 3.8 12.3 - - + -
320B TRP* 1.3 77.2 - - - +
322B THR* 1.3 65.3 + - - +
327B ILE* 3.7 0.7 - - - -
328B TYR* 2.8 37.4 + - + +
330B VAL* 3.9 14.8 - - + -
378B ILE* 4.1 24.7 - - + +
381B VAL* 4.0 24.7 - - + -
382B LEU* 3.9 21.1 - - + -
385B TRP* 3.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.9 19.2 - - + +
274B TRP* 4.8 10.8 - - + -
289B PHE* 5.6 1.8 - - + -
299B VAL* 3.8 3.0 - - - -
300B MET* 2.9 52.3 + - + +
302B PHE* 5.8 3.4 - - + -
320B TRP 5.8 0.4 - - - -
321B LEU* 1.3 76.6 - - - +
323B ASP* 1.3 58.2 + - - +
324B ASN* 2.9 18.4 + - - +
326B ARG 2.7 22.7 + - - -
327B ILE* 3.7 17.4 - - + +
385B TRP* 4.1 4.7 - - - -
----------------------------------------------------------
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