Contacts of the helix formed by residues 340 - 354 (chain B) in PDB entry 2N97
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 PRO 340 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER 3.9 2.2 - - - +
339B LEU* 1.3 95.4 - - + +
341B PRO* 1.3 75.7 - - + +
342B ALA* 4.4 7.6 - - + +
343B LYS* 3.1 34.8 + - + +
344B ARG* 3.4 10.0 + - - +
425B SER 5.4 0.2 - - - +
426B PRO* 4.2 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU 4.6 0.7 - - - +
340B PRO* 1.3 87.4 - - + +
342B ALA* 1.3 56.5 + - - +
344B ARG* 3.1 27.9 + - + +
345B GLU* 3.0 35.4 + - + +
426B PRO 3.5 19.1 - - - +
427B VAL* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO* 3.3 6.9 - - + -
341B PRO* 1.3 80.5 - - + +
343B LYS* 1.3 59.1 + - - +
345B GLU* 3.7 10.0 + - - +
346B GLU* 3.5 24.3 + - - +
423B ALA* 4.9 14.8 - - + -
425B SER 4.4 16.8 - - - +
426B PRO 5.8 1.3 - - - -
427B VAL 5.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.1 36.8 - - + +
340B PRO* 3.1 29.8 + - + +
342B ALA* 1.3 73.8 - - + +
344B ARG* 1.3 64.7 + - - +
346B GLU* 3.3 18.1 + - + +
347B VAL* 3.4 17.2 + - - +
417B LEU* 3.2 36.2 + - - +
420B GLU* 4.6 4.1 - - - +
421B SER* 3.3 41.3 + - - +
423B ALA* 5.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.4 48.3 + - + +
337B SER* 5.6 4.6 + - - +
339B LEU* 4.6 14.0 + - + +
340B PRO 3.6 13.9 - - - +
341B PRO* 3.1 27.9 + - - +
343B LYS* 1.3 71.7 - - - +
345B GLU* 1.3 65.3 + - + +
347B VAL* 3.2 6.8 + - - +
348B GLU* 3.2 23.9 + - - +
387B LEU* 5.2 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PRO* 3.0 23.3 + - + +
342B ALA* 3.8 9.2 - - - +
344B ARG* 1.3 77.3 - - - +
346B GLU* 1.3 56.3 + - + +
348B GLU* 3.4 21.8 + - - +
349B LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA 3.5 12.7 + - - +
343B LYS* 3.3 15.7 + - + +
345B GLU* 1.3 74.4 - - + +
347B VAL* 1.3 60.1 + - - +
349B LYS* 3.7 25.4 + - - +
350B LEU* 3.0 38.2 + - + +
417B LEU* 4.8 5.2 - - + -
420B GLU* 3.8 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.7 27.6 - - + +
339B LEU* 6.2 0.9 - - + -
343B LYS* 3.4 14.8 + - - +
344B ARG 3.2 6.4 + - - +
346B GLU* 1.3 75.8 - - - +
348B GLU* 1.3 61.7 + - - +
350B LEU* 3.6 1.6 + - - +
351B LEU* 3.4 32.6 + - + +
383B VAL* 4.3 8.7 - - + +
387B LEU* 3.9 24.0 - - + -
401B LEU* 6.5 1.1 - - + -
413B LEU* 6.0 0.7 - - + -
417B LEU* 3.9 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG 3.2 11.8 + - - +
345B GLU* 3.5 23.8 - - - +
346B GLU 3.3 0.2 - - - -
347B VAL* 1.3 76.5 - - - +
349B LYS* 1.3 56.7 + - - +
351B LEU* 3.3 3.1 + - - +
352B ASN* 2.8 32.2 + - + +
381B CYS* 3.6 30.1 - - - +
383B VAL* 4.0 21.1 - - + +
384B ARG* 3.7 33.0 + - + +
387B LEU* 5.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLU 2.9 20.6 + - - +
346B GLU* 3.3 28.7 + - - +
348B GLU* 1.3 71.5 - - - +
350B LEU* 1.3 58.3 - - - +
352B ASN* 4.2 14.8 - - - +
353B GLY* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 3.0 18.8 + - + +
347B VAL* 3.8 5.4 - - - +
348B GLU 3.4 0.2 - - - -
349B LYS* 1.3 77.1 - - - +
351B LEU* 1.3 60.2 + - + +
354B SER* 2.9 51.8 + - - +
355B ALA 3.5 1.9 + - - -
413B LEU* 3.9 23.8 - - + -
416B SER* 4.0 29.8 - - - +
417B LEU* 3.5 34.5 - - + +
420B GLU* 4.9 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS 3.9 2.6 - - - +
380A ALA* 4.8 3.2 + - - -
347B VAL* 3.4 24.7 + - + +
348B GLU 3.3 3.8 + - - +
350B LEU* 1.3 81.7 - - + +
352B ASN* 1.3 62.9 + - - +
353B GLY 3.6 0.2 + - - -
355B ALA 3.6 16.9 - - - +
356B GLY* 3.0 31.5 + - - -
358B THR* 3.7 21.8 - - - +
359B TRP* 4.0 31.6 - - + +
383B VAL* 4.0 30.3 - - + -
413B LEU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS 4.6 1.1 - - - +
379A GLU* 3.7 19.8 - - - +
380A ALA* 3.6 30.4 + - + +
348B GLU* 2.8 23.1 + - + +
349B LYS* 3.4 16.2 + - - +
351B LEU* 1.3 73.9 - - - +
353B GLY* 1.3 56.9 + - - +
381B CYS* 5.3 5.5 - - - -
383B VAL* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS 5.1 1.8 - - - -
379A GLU* 4.8 6.3 - - - +
349B LYS* 2.9 22.8 + - - -
352B ASN* 1.3 81.5 - - - +
354B SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 4.2 14.1 - - - +
350B LEU* 2.9 32.0 + - - +
353B GLY* 1.3 77.8 - - - +
355B ALA* 1.3 62.9 + - - +
----------------------------------------------------------
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