Contacts of the strand formed by residues 351 - 360 (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 LYS 351 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B TYR* 3.2 8.1 - - - -
348B LYS 3.0 28.3 + - - +
349B ASP* 3.9 8.5 + - + +
350B ASP* 1.3 87.6 + - - +
352B LEU* 1.3 62.3 + - - +
353B TYR* 3.5 32.4 - - + +
372B VAL* 5.8 8.5 - - + -
375B LEU* 4.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 5.9 0.9 - - + -
301B LEU* 3.7 17.7 - - + -
319B LEU* 4.4 9.0 - - + -
345B VAL* 3.4 24.9 - - + -
346B LEU 3.7 7.0 - - - +
347B TYR* 3.9 17.5 - - + -
351B LYS* 1.3 75.9 - - - +
353B TYR* 1.3 66.7 + - - +
370B ARG* 3.7 2.3 - - - -
371B LEU* 2.8 63.7 + - + +
374B GLU* 4.6 3.6 - - + -
375B LEU* 4.2 18.1 - - + +
378B ILE* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.0 11.9 - - + -
46B MET* 4.8 6.1 - - + -
73B ASP* 3.7 32.8 + - + +
345B VAL* 3.4 10.2 - - - +
346B LEU* 2.7 46.8 + - + +
348B LYS* 4.1 16.2 + - + -
351B LYS* 3.5 44.7 - - + +
352B LEU* 1.3 78.1 - - - +
354B CYS* 1.3 61.6 + - - +
368B PHE* 3.3 30.5 - + + -
369B ALA 3.1 10.5 - - - +
370B ARG* 3.6 32.0 + - + -
371B LEU* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.3 3.1 - - - -
303B THR* 5.4 1.6 - - - -
317B LEU* 4.3 6.7 - - - -
333B VAL* 4.5 6.1 - - + -
343B SER* 4.1 11.9 - - - -
344B SER 3.3 14.8 - - - -
345B VAL* 4.3 9.4 - - + -
353B TYR* 1.3 76.6 - - - +
355B LEU* 1.3 70.7 + - - +
356B HIS* 4.0 19.0 + - + -
367B VAL 3.7 1.7 - - - +
368B PHE* 3.6 2.2 - - - -
369B ALA* 2.7 42.8 + - + +
371B LEU* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.3 3.1 - - + -
11B PHE* 4.2 11.4 - - + -
37B PRO* 3.5 26.9 - - + +
38B ALA 4.1 14.6 - - - +
39B LEU* 3.9 20.7 - - + +
48B ALA* 3.8 24.2 - - + -
49B ILE 4.9 1.6 - - - +
343B SER* 3.3 1.7 - - - -
344B SER* 2.9 31.9 + - - +
354B CYS* 1.3 70.3 - - - +
356B HIS* 1.3 62.5 + - - +
366B LEU* 4.0 23.6 - - + -
367B VAL 3.4 15.9 - - - +
368B PHE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 3.8 19.9 + - - -
37B PRO* 4.5 2.0 - - - -
317B LEU* 3.6 28.4 - - + +
333B VAL* 4.3 9.6 + - + +
334B SER* 4.0 21.1 - - - -
338B GLU* 3.9 4.7 - - - -
340B SER* 4.0 2.4 - - - -
342B TYR 3.4 12.1 - - - +
343B SER* 3.8 3.4 - - - -
354B CYS* 4.0 13.7 - - + -
355B LEU* 1.3 75.7 - - - +
357B GLU* 1.3 81.9 + - - +
358B ILE* 3.8 5.6 - - + -
366B LEU* 3.0 9.5 - - - -
367B VAL* 2.8 68.8 + - + +
369B ALA* 5.1 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE 4.5 2.2 - - - +
35B ARG* 2.7 48.8 + - - +
36B LEU 3.1 20.1 + - - -
37B PRO* 4.1 1.3 - - + -
340B SER* 3.1 16.2 - - - -
341B ALA* 3.6 7.5 - - - +
342B TYR* 2.9 46.4 + - + +
356B HIS* 1.3 87.6 + - - +
358B ILE* 1.3 61.2 + - - +
359B ASN* 5.8 0.2 - - + -
364B TYR* 4.1 11.8 - - + -
365B SER 3.2 7.4 - - - +
366B LEU* 3.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 3.7 19.7 - - - +
9B GLU* 4.7 7.0 - - + +
13B ARG* 3.3 28.4 + - - +
338B GLU* 3.3 37.7 - - + +
339B ASN 3.3 4.5 - - - +
356B HIS* 3.8 10.7 + - + -
357B GLU* 1.3 81.3 - - - +
359B ASN* 1.3 59.6 + - - +
364B TYR* 3.3 4.7 - - - +
365B SER* 2.9 48.3 + - - +
367B VAL* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP 5.4 1.4 - - - +
313B LEU* 4.4 7.8 - - - +
339B ASN* 2.9 56.9 + - + +
340B SER* 5.9 0.2 - - - -
341B ALA 6.2 0.7 - - - +
357B GLU* 5.8 0.7 - - + -
358B ILE* 1.3 75.5 - - - +
360B SER* 1.3 65.4 + - - +
361B ASN 3.5 0.8 - - - +
362B GLU* 2.7 57.3 - - - +
363B VAL 3.4 5.2 - - - +
364B TYR* 3.5 31.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.3 23.0 + - - +
339B ASN* 4.9 1.3 - - - +
359B ASN* 1.3 73.0 + - - +
361B ASN* 1.3 81.2 + - - +
362B GLU 3.2 1.3 - - - -
363B VAL* 2.9 27.0 + - - +
----------------------------------------------------------
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