Contacts of the strand formed by residues 352 - 362 (chain A) in PDB entry 5EMV
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 352 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.7 1.6 - - - -
348A CYS* 3.2 4.2 - - - -
349A SER 2.9 32.4 + - - +
350A PHE* 4.0 13.5 - - + +
351A GLY* 1.3 81.0 - - - +
353A GLN* 1.3 67.3 + - - +
354A VAL* 3.4 4.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.2 16.9 - - + +
346A LYS* 3.3 35.7 - - + +
347A VAL 3.6 6.1 - - - +
348A CYS* 4.1 6.7 - - - -
352A LYS* 1.3 74.1 - - - +
354A VAL* 1.3 64.2 + - - +
355A VAL 3.7 17.0 - - - +
356A GLU* 3.3 30.7 + - - +
355B VAL* 3.8 28.5 - - + +
356B GLU 4.7 1.4 - - - +
357B LYS* 5.6 0.2 - - - +
380B P1L 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 2.9 24.6 + - + +
348A CYS* 4.5 2.0 - - - +
349A SER* 3.9 17.9 - - - +
352A LYS* 3.8 11.4 - - + +
353A GLN* 1.3 78.8 - - - +
355A VAL* 1.3 73.0 + - + +
382A TYR* 3.7 40.6 - - + +
353B GLN* 3.6 4.4 + - + -
354B VAL 3.9 18.2 - - - +
355B VAL* 3.5 4.3 - - - +
356B GLU 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A SER 4.2 0.7 - - - +
346A LYS* 3.2 4.2 - - - -
347A VAL* 2.7 43.5 + - + +
353A GLN* 3.6 6.6 - - - +
354A VAL* 1.3 101.5 - - + +
356A GLU* 1.3 69.1 + - - +
357A LYS* 4.7 1.6 - - + +
380A P1L 4.2 26.5 - - + -
382A TYR* 3.9 27.8 - - + -
353B GLN* 4.0 0.4 - - - +
356B GLU* 3.4 30.3 - - - +
358B VAL* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 2.8 27.6 + - - +
345A SER 3.4 3.6 - - - +
346A LYS* 3.9 22.9 + - + -
353A GLN* 3.3 25.7 + - - +
355A VAL* 1.3 74.4 - - - +
357A LYS* 1.3 63.0 + - - +
358A VAL* 3.7 16.8 - - + +
356B GLU 3.0 6.8 + - - +
357B LYS* 3.4 23.7 + - + +
358B VAL* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 5.6 1.8 - - - +
343A CYS 3.6 1.6 - - - +
344A SER* 3.4 2.4 - - - -
345A SER* 2.8 41.6 + - - +
355A VAL* 4.2 2.0 - - + -
356A GLU* 1.3 73.6 - - - +
358A VAL* 1.3 65.2 + - - +
359A GLU* 4.1 20.3 + - + +
377A SER* 2.9 29.9 + - - -
378A PRO* 3.4 17.4 + - - +
379A MET* 5.1 0.2 - - - +
380A P1L 3.2 47.1 - - + +
358B VAL* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 3.9 26.0 - - + -
343A CYS 3.3 5.2 - - - +
344A SER* 4.2 6.7 - - - +
356A GLU* 3.7 26.9 - - + +
357A LYS* 1.3 79.6 - - - +
359A GLU* 1.3 70.4 + - - +
360A THR* 5.4 1.8 - - - +
357B LYS* 4.2 14.1 - - - -
358B VAL* 3.0 11.7 + - - +
359B GLU* 4.1 8.1 - - + -
360B THR* 3.9 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 3.6 2.4 - - - -
343A CYS* 2.9 37.1 + - + +
357A LYS* 4.1 21.0 + - + +
358A VAL* 1.3 81.5 - - - +
360A THR* 1.3 68.6 + - - +
374A LEU* 3.7 29.2 - - + +
377A SER* 2.9 32.3 + - - -
378A PRO* 5.5 0.5 - - - +
360B THR* 5.0 11.9 - - - +
415B ARG* 5.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 3.7 21.1 - - + -
341A LEU 3.3 11.3 + - - +
342A THR* 4.6 8.4 + - - +
358A VAL* 5.4 2.1 - - - +
359A GLU* 1.3 82.4 + - - +
361A GLU* 1.3 71.3 + - - +
374A LEU* 5.1 1.4 - - - +
415A ARG* 4.6 14.4 - - - +
360B THR* 5.7 6.1 + - - +
415B ARG* 4.9 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 4.4 2.9 - - - -
341A LEU* 3.0 37.5 + - + +
360A THR* 1.3 78.9 - - - +
362A ARG* 1.3 79.1 + - - +
364A GLN* 5.7 2.6 - - - +
371A VAL 5.2 0.3 - - - +
372A TYR* 3.8 13.9 - - + -
373A ARG* 3.4 43.0 + - - +
374A LEU* 4.0 22.4 - - + +
415B ARG* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A HIS* 5.7 3.4 - - + +
339A MET 4.2 4.5 - - - +
340A THR* 4.2 15.9 - - + +
360A THR* 5.2 0.4 - - - +
361A GLU* 1.3 96.0 - - - +
363A ALA* 1.3 70.2 + - - +
364A GLN* 3.6 2.1 + - - +
371A VAL 4.2 1.7 - - - +
372A TYR* 4.0 2.8 - - - -
----------------------------------------------------------
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