Contacts of the helix formed by residues 344 - 356 (chain B) in PDB entry 1N78
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 SER 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B TRP* 3.2 19.6 - - - -
343B GLU* 1.3 87.7 + - - +
345B GLU* 1.3 63.8 + - - +
346B ALA* 3.5 8.2 + - - +
347B TYR* 3.0 23.6 + - - +
348B LEU 3.1 16.6 + - - -
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ALA* 6.1 0.9 - - - +
329B GLU* 3.5 9.9 - - - +
332B LYS* 3.0 34.6 + - - -
342B TRP* 3.3 20.7 + - - -
344B SER* 1.3 71.3 - - - +
346B ALA* 1.3 67.8 + - - +
348B LEU* 3.4 6.1 + - - +
349B ARG* 2.9 34.0 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B SER* 3.3 7.7 + - - +
345B GLU* 1.3 80.4 - - - +
347B TYR* 1.3 61.7 + - - +
349B ARG* 3.5 9.4 + - - +
350B ARG* 3.1 23.4 + - - +
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B TRP* 4.9 0.2 - - + -
343B GLU* 3.6 37.9 - - + +
344B SER* 3.0 22.3 + - - +
346B ALA* 1.3 76.5 - - - +
348B LEU* 1.3 66.0 + - - +
350B ARG* 3.0 8.4 + - - +
351B ALA* 2.9 25.2 + - + +
372B LEU* 2.7 36.3 + - - +
373B PHE* 4.1 20.4 - + - -
453B LEU* 3.5 48.1 - - + +
454B LEU* 4.6 7.3 - - - +
458B ARG* 4.0 21.2 + - - -
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ALA* 3.7 16.6 - - + +
331B VAL* 4.6 0.7 - - + -
332B LYS* 3.7 36.3 - - + -
335B LEU* 3.7 25.1 - - + -
342B TRP* 3.8 20.4 - - + +
344B SER 3.1 15.6 + - - +
345B GLU* 3.7 7.6 - - - +
347B TYR* 1.3 83.9 - - - +
349B ARG* 1.3 53.6 + - - +
351B ALA* 3.1 3.4 + - - +
352B VAL* 2.8 54.1 + - + +
365B PHE* 4.4 0.2 - - + -
373B PHE* 3.8 19.7 - - + -
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 3.4 35.8 - - + +
325B GLU* 3.7 36.2 + - - +
328B ALA* 4.5 10.9 - - + +
345B GLU* 2.9 23.9 + - - +
346B ALA* 3.7 7.8 - - - +
348B LEU* 1.3 75.9 - - - +
350B ARG* 1.3 57.8 + - - +
352B VAL* 3.4 2.6 + - - -
353B GLU* 2.9 27.4 + - - +
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ALA 3.1 12.7 + - - +
347B TYR* 3.0 9.2 + - - +
349B ARG* 1.3 76.2 - - - +
351B ALA* 1.3 62.6 + - - +
353B GLU* 2.8 42.8 + - - +
354B LEU* 3.1 44.4 + - + +
409B GLU* 2.8 30.9 + - - -
449B GLU* 3.5 20.2 + - - +
453B LEU* 3.5 27.5 - - + +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B TYR* 2.9 19.7 + - + +
348B LEU* 3.5 7.6 - - - +
350B ARG* 1.3 77.8 - - - +
352B VAL* 1.3 63.8 + - - +
354B LEU* 3.4 4.1 + - - +
355B MET* 3.2 24.9 + - - +
365B PHE* 3.9 3.9 - - + -
372B LEU* 4.1 19.0 - - + +
373B PHE* 3.7 29.2 - - + -
453B LEU* 4.4 10.5 - - + +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 3.7 18.4 - - + -
327B VAL* 3.6 31.6 - - + -
328B ALA* 4.0 17.9 - - + +
331B VAL* 4.6 6.7 - - + -
348B LEU* 2.8 31.8 + - + +
349B ARG* 3.6 5.2 - - - +
351B ALA* 1.3 77.2 - - - +
353B GLU* 1.3 56.6 + - - +
355B MET* 3.3 1.6 + - - +
356B ARG* 2.9 30.8 + - + +
359B PHE* 4.5 3.7 - - + -
365B PHE* 3.8 25.1 - - + -
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 4.1 28.7 - - + +
349B ARG* 2.9 17.6 + - - +
350B ARG* 2.8 39.3 + - - +
351B ALA 3.2 0.2 - - - -
352B VAL* 1.3 78.7 - - - +
354B LEU* 1.3 63.4 + - + +
355B MET 3.2 0.5 + - - -
356B ARG* 3.4 16.7 + - - +
357B PRO* 4.1 4.2 - - - +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ARG* 3.1 47.2 + - - +
351B ALA* 3.4 4.9 + - - +
353B GLU* 1.3 75.9 - - + +
355B MET* 1.3 57.8 + - - +
356B ARG 3.6 0.4 + - - -
357B PRO* 4.0 1.2 - - - +
358B ARG* 2.8 29.3 + - - -
372B LEU* 5.5 2.2 - - + -
445B PRO* 3.5 20.1 - - + +
449B GLU* 3.5 48.0 - - + +
450B ILE* 4.4 13.9 - - + -
453B LEU* 4.1 20.0 - - + -
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ALA 3.2 16.5 + - - +
352B VAL 3.9 1.1 - - - +
353B GLU 3.1 0.6 - - - -
354B LEU* 1.3 77.6 - - - +
356B ARG* 1.3 58.0 + - - +
357B PRO* 3.3 3.8 - - - -
358B ARG* 2.8 45.7 + - + -
359B PHE* 3.0 20.0 - - + -
365B PHE* 3.4 30.5 - - + +
368B LYS* 3.4 41.3 - - + +
369B ALA* 3.8 13.9 - - + -
371B TYR* 4.2 8.5 - - - +
372B LEU* 4.9 4.3 - - - -
443B GLU 5.4 4.7 - - - +
445B PRO* 3.9 23.8 - - + -
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Residues in contact with ARG 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 2.9 48.2 + - + +
319B ARG* 3.6 31.4 + - + +
322B LEU 3.1 24.5 + - - -
323B SER* 4.1 3.8 - - - +
324B LEU* 4.0 29.7 - - - +
327B VAL* 4.3 8.3 - - + +
352B VAL* 2.9 28.7 + - + +
353B GLU* 3.4 10.7 + - - +
355B MET* 1.3 75.4 - - - +
357B PRO* 1.3 67.5 - - + +
358B ARG 3.2 2.9 + - - -
359B PHE* 3.9 19.1 - - + +
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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