Contacts of the helix formed by residues 340 - 354 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A SER 3.9 1.8 - - - +
339A LEU* 1.4 98.2 - - + +
341A PRO* 1.3 75.9 - - + +
342A ALA* 4.4 6.5 - - + +
343A LYS* 3.1 32.3 + - + +
344A ARG* 3.4 9.9 + - - +
423A ALA* 6.2 2.7 - - + -
426A PRO* 4.9 18.2 - - + -
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Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU 4.5 1.1 - - - +
340A PRO* 1.3 86.2 - - + +
342A ALA* 1.3 56.5 + - - +
344A ARG* 3.2 13.2 + - + +
345A GLU* 2.9 35.2 + - + +
426A PRO* 5.4 1.1 - - + -
427A VAL* 4.2 35.2 - - + +
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PRO* 3.2 7.6 - - + -
341A PRO* 1.3 79.9 - - - +
343A LYS* 1.3 58.8 + - - +
345A GLU* 3.6 9.3 - - - +
346A GLU* 3.3 24.1 + - - +
423A ALA* 5.7 8.5 - - + -
425A SER* 3.5 28.7 - - - +
426A PRO* 5.2 0.2 - - + -
427A VAL* 5.0 7.9 - - + +
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 4.8 0.9 - - - -
339A LEU* 4.3 30.2 - - + +
340A PRO* 3.1 33.2 + - + +
342A ALA* 1.3 73.9 - - - +
344A ARG* 1.3 63.7 + - - +
346A GLU* 3.2 18.2 + - + +
347A VAL* 3.2 22.0 + - - +
417A LEU* 3.8 29.2 + - - +
420A GLU* 3.7 24.0 - - + +
421A SER* 3.6 32.1 - - - +
423A ALA* 5.3 7.2 - - + -
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Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 3.5 53.6 + - + +
337A SER* 5.2 4.4 - - - +
339A LEU* 4.7 11.7 - - + +
340A PRO 3.6 14.1 - - - +
341A PRO* 3.2 12.0 + - + +
343A LYS* 1.3 71.7 - - - +
345A GLU* 1.3 63.4 + - - +
347A VAL* 3.3 4.3 + - - +
348A GLU* 3.1 27.6 + - - +
384A ARG 5.5 1.6 + - - -
387A LEU* 4.0 25.6 + - + +
388A ALA* 5.0 12.3 - - - +
391A ALA* 4.1 13.5 - - - +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A PRO* 2.9 21.3 + - + +
342A ALA* 3.6 11.0 - - - +
344A ARG* 1.3 76.3 - - - +
346A GLU* 1.3 55.8 + - - +
348A GLU* 3.4 21.8 + - - +
349A LYS* 2.9 29.6 + - - +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ALA 3.3 13.1 + - - +
343A LYS* 3.2 15.7 + - + +
345A GLU* 1.3 74.6 - - - +
347A VAL* 1.3 60.6 + - - +
349A LYS* 3.3 23.7 + - - +
350A LEU* 3.0 47.1 + - + +
417A LEU* 5.0 3.6 - - + -
420A GLU* 3.9 43.5 - - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A TYR* 3.4 32.1 - - + +
343A LYS* 3.2 16.1 + - - +
344A ARG 3.3 3.1 + - - +
346A GLU* 1.3 74.8 - - - +
348A GLU* 1.3 62.8 + - - +
350A LEU* 3.6 2.3 + - - +
351A LEU* 3.3 32.1 + - + +
383A VAL* 4.4 8.5 - - + +
387A LEU* 4.0 22.7 - - + -
417A LEU* 3.8 34.5 - - + -
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ARG 3.1 17.0 + - - +
345A GLU* 3.6 23.5 - - - +
347A VAL* 1.3 75.6 - - - +
349A LYS* 1.3 57.2 + - - +
351A LEU* 3.2 4.0 + - - +
352A ASN* 2.8 32.5 + - + +
381A CYS* 3.9 19.2 - - - +
383A VAL* 4.2 23.1 - - + +
384A ARG* 3.7 35.3 + - + +
387A LEU* 4.8 6.5 - - + -
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A GLU 2.9 20.4 + - - +
346A GLU* 3.3 24.8 + - - +
348A GLU* 1.3 72.0 - - - +
350A LEU* 1.3 60.5 + - - +
352A ASN* 3.8 8.9 - - + +
353A GLY* 2.9 33.8 + - - -
354A SER* 4.2 4.9 + - - -
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLU* 3.0 28.1 + - + +
347A VAL* 3.7 5.6 - - - +
349A LYS* 1.3 78.9 - - - +
351A LEU* 1.3 63.1 + - + +
354A SER* 2.9 51.9 + - - +
355A ALA 3.4 4.3 + - - +
413A LEU* 3.9 21.3 - - + -
416A SER* 4.6 19.7 - - - +
417A LEU* 3.5 33.9 - - + +
420A GLU* 5.9 2.0 - - + -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A VAL* 3.3 27.3 + - + +
348A GLU 3.2 6.9 + - - +
350A LEU* 1.3 82.6 - - + +
352A ASN* 1.3 62.1 + - - +
355A ALA 3.5 16.4 - - - +
356A GLY* 3.2 30.6 + - - -
358A THR* 3.6 22.4 - - - +
359A TRP* 3.9 37.0 - - + +
383A VAL* 4.1 24.0 - - + -
413A LEU* 5.0 9.6 - - + -
378B HIS 3.9 4.0 - - - +
380B ALA* 4.7 4.6 + - - -
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Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A GLU* 2.8 23.6 + - + +
349A LYS* 3.8 11.3 - - - +
351A LEU* 1.3 73.7 - - - +
353A GLY* 1.3 57.3 + - - +
381A CYS* 4.2 13.3 - - - -
383A VAL* 5.8 0.8 - - - +
378B HIS 4.8 0.7 - - - -
379B GLU* 3.6 18.2 - - - +
380B ALA* 3.5 34.7 + - - +
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LYS* 2.9 21.3 + - - -
352A ASN* 1.3 81.3 - - - +
354A SER* 1.3 64.0 + - - +
378B HIS 4.9 2.0 - - - -
379B GLU* 4.7 6.4 - - - +
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LYS* 4.2 5.9 + - - -
350A LEU* 2.9 37.6 + - - +
353A GLY* 1.3 74.3 - - - +
355A ALA* 1.3 63.6 + - - +
378B HIS* 3.7 17.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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