Contacts of the helix formed by residues 357 - 369 (chain B) in PDB entry 2R5N
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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B ILE 3.6 2.4 + - - -
356B ALA* 1.3 73.2 - - - +
358B ARG* 1.3 56.8 + - - +
360B ALA* 3.6 8.1 - - - +
361B SER* 2.8 29.3 + - - -
493B PRO* 4.3 6.2 + - - -
495B ASP 4.9 2.7 - - - -
499B SER* 3.4 19.7 + - - -
517B ILE 4.4 1.7 + - - -
518B LEU* 3.3 19.5 - - - +
519B SER* 2.7 37.9 + - - -
523B LEU* 3.7 17.5 - - - +
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Residues in contact with ARG 358 (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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356B ALA* 3.1 8.6 - - + +
357B SER* 1.3 77.7 + - - +
359B LYS* 1.3 59.9 + - - +
361B SER* 3.3 6.9 - - - -
362B GLN 3.1 20.8 + - - -
384B PRO 4.7 2.4 + - - -
385B SER* 2.9 27.7 + - - +
386B ASN 4.1 4.1 - - - +
387B LEU* 3.8 27.0 - - + +
460B THR* 3.7 22.9 - - + -
461B HIS* 3.4 15.1 + - - -
518B LEU* 3.9 8.1 - - + +
519B SER 3.2 20.7 + - - +
520B ARG* 3.6 35.2 + - - +
681B RP5 2.9 30.9 + - - -
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Residues in contact with LYS 359 (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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355B ILE* 4.1 23.1 - - + -
356B ALA* 2.9 17.7 + - + +
358B ARG* 1.3 80.0 - - + +
360B ALA* 1.3 59.8 + - - +
361B SER 3.1 0.2 - - - -
362B GLN* 3.0 31.3 + - - +
363B ASN* 2.8 61.8 + - - +
387B LEU* 3.8 14.4 - - + -
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Residues in contact with ALA 360 (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 PHE* 5.6 0.5 - - - -
348B LEU* 6.1 0.5 - - - +
355B ILE* 3.7 10.4 - - + +
356B ALA 2.9 7.3 + - - +
357B SER* 3.3 10.1 + - - +
359B LYS* 1.3 76.7 - - - +
361B SER* 1.3 56.8 + - - +
363B ASN* 3.3 7.0 + - - +
364B ALA* 3.0 27.9 + - - +
496B GLN* 3.5 28.4 - - + +
499B SER* 3.5 31.5 - - - +
500B ALA* 5.3 0.5 + - - +
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Residues in contact with SER 361 (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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357B SER 2.8 17.0 + - - -
358B ARG 3.3 10.5 - - - -
360B ALA* 1.3 70.6 - - - +
362B GLN* 1.3 66.4 + - - +
364B ALA* 3.0 5.4 + - - +
365B ILE* 2.9 27.0 + - - +
386B ASN 5.4 1.3 - - - -
387B LEU 5.2 0.7 + - - -
458B VAL* 3.7 12.0 - - - +
499B SER* 4.6 2.6 - - - -
503B TRP* 2.9 33.1 + - - +
518B LEU* 3.5 25.7 - - - +
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Residues in contact with GLN 362 (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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358B ARG 3.1 4.3 + - - +
359B LYS* 3.0 39.6 + - - +
361B SER* 1.3 78.3 + - - +
363B ASN* 1.3 57.7 + - - +
365B ILE* 3.2 8.2 + - + +
366B GLU* 2.9 29.5 + - + +
387B LEU* 3.3 51.8 + - + +
389B LEU* 2.9 30.8 + - - +
390B TRP* 4.9 1.5 - - - +
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Residues in contact with ASN 363 (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 PHE* 3.7 15.1 - - + -
348B LEU* 6.0 3.9 - - + +
355B ILE* 3.5 24.7 - - - +
359B LYS* 2.8 47.3 + - - +
360B ALA* 3.5 8.0 - - - +
361B SER 3.2 0.2 - - - -
362B GLN* 1.3 75.0 - - - +
364B ALA* 1.3 58.6 + - - +
366B GLU* 3.4 7.5 + - - +
367B ALA* 2.9 28.2 + - - +
496B GLN* 4.6 5.8 + - - +
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Residues in contact with ALA 364 (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 PHE* 4.0 20.3 - - + -
360B ALA 3.0 10.6 + - - +
361B SER 3.0 8.8 + - - +
363B ASN* 1.3 72.8 - - - +
365B ILE* 1.3 61.1 + - - +
367B ALA 3.2 0.7 + - - -
368B PHE* 2.8 42.5 + - + -
500B ALA* 4.5 9.4 - - - -
503B TRP* 3.7 32.8 - - + -
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Residues in contact with ILE 365 (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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361B SER* 2.9 23.4 + - - +
362B GLN* 3.5 7.2 - - + +
364B ALA* 1.3 76.7 - - - +
366B GLU* 1.3 52.7 + - - +
368B PHE* 3.7 0.8 - - - +
369B GLY* 2.7 33.4 + - - -
375B PHE* 4.2 10.7 - - + -
387B LEU 4.1 15.9 - - - +
388B THR* 4.1 20.0 - - + +
390B TRP* 3.5 32.8 - - + +
430B TYR* 3.6 26.0 - - + +
458B VAL* 5.3 1.6 - - + -
503B TRP* 3.5 33.2 - - + -
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Residues in contact with GLU 366 (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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362B GLN* 2.9 15.9 + - + +
363B ASN* 3.5 12.8 - - - +
365B ILE* 1.3 77.4 - - - +
367B ALA* 1.3 61.3 + - - +
370B PRO* 3.2 21.5 - - - +
390B TRP* 3.3 19.4 - - + +
391B SER* 2.6 49.8 + - - -
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Residues in contact with ALA 367 (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 PHE* 3.7 41.7 - - + -
363B ASN 2.9 17.9 + - - +
364B ALA 3.2 3.3 + - - +
366B GLU* 1.3 78.8 - - - +
368B PHE* 1.3 65.2 + - + +
370B PRO* 3.6 8.7 - - - +
371B LEU* 3.9 15.0 - - - +
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Residues in contact with PHE 368 (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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337B PHE* 3.8 28.0 - + - -
341B ALA* 3.9 26.0 - - + -
344B PHE* 4.3 20.4 - + + -
345B ILE* 5.8 0.9 - - + -
364B ALA* 2.8 23.2 + - + +
367B ALA* 1.3 82.2 - - + +
369B GLY* 1.3 66.1 + - - +
370B PRO 3.4 0.4 - - - -
371B LEU* 2.9 22.1 + - + +
372B LEU* 2.9 18.2 + - + +
375B PHE* 3.9 16.8 - + + -
500B ALA* 4.2 6.7 - - + -
503B TRP* 3.8 28.7 - + + -
504B LYS* 3.7 30.5 - - + -
507B VAL* 4.2 7.2 - - + -
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Residues in contact with GLY 369 (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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365B ILE 2.7 21.1 + - - -
368B PHE* 1.3 74.0 - - - +
370B PRO* 1.4 68.2 - - - +
371B LEU 3.1 1.2 + - - -
372B LEU 3.3 17.2 + - - +
373B PRO* 4.1 2.8 - - - +
375B PHE* 4.1 11.0 - - - -
390B TRP* 3.4 30.8 - - - -
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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