Contacts of the helix formed by residues 357 - 372 (chain B) in PDB entry 2X1L
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 LEU 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B ASP 3.3 11.0 + - - +
353B LEU* 3.7 8.1 - - + +
356B GLU* 1.3 78.4 - - - +
358B GLY* 1.3 67.7 + - - +
359B ASN 3.5 0.4 - - - -
360B LEU* 3.6 5.0 + - + +
361B ALA* 3.2 23.8 + - + +
417B TRP* 3.8 28.7 - - + -
420B LEU* 3.9 28.3 - - + -
458B VAL* 5.3 7.4 - - + -
461B ALA* 5.1 4.3 - - + -
462B SER* 5.6 0.7 - - - +
465B LEU* 4.0 15.7 - - + -
469B MET* 4.2 3.4 - - + -
476B LEU* 4.5 16.4 - - + -
509B PHE* 3.7 33.2 - - + -
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Residues in contact with GLY 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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353B LEU 2.7 22.0 + - - -
354B ALA* 3.4 7.3 + - - -
357B LEU* 1.3 74.4 - - - +
359B ASN* 1.3 59.4 + - - +
361B ALA* 3.8 4.3 - - - +
362B GLN* 3.0 28.6 + - - +
508B ILE* 6.1 1.8 - - - -
509B PHE* 4.1 20.2 - - - -
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Residues in contact with ASN 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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354B ALA 3.1 19.5 + - - +
355B ASN* 3.1 37.3 + - - +
358B GLY* 1.3 74.4 - - - +
360B LEU* 1.3 58.5 + - - +
362B GLN* 4.3 9.0 - - - +
363B ARG* 2.8 48.1 + - + +
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASN 3.7 3.0 + - - -
356B GLU 3.4 16.2 - - - +
357B LEU* 3.6 3.5 + - + +
358B GLY 3.4 0.8 - - - -
359B ASN* 1.3 77.6 - - - +
361B ALA* 1.3 57.5 + - - +
363B ARG* 4.4 5.7 - - - +
364B SER* 2.8 27.4 + - - -
420B LEU* 3.9 34.5 - - + +
423B ALA* 4.0 23.1 - - + +
424B ASN* 3.4 36.2 + - - +
427B PHE* 4.5 10.5 - - + -
454B THR* 4.0 19.5 - - + -
458B VAL* 4.1 15.5 - - + -
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.2 16.2 + - + +
358B GLY* 3.8 5.2 - - - +
360B LEU* 1.3 78.1 - - - +
362B GLN* 1.3 58.8 + - - +
364B SER* 2.9 18.3 + - - -
365B LEU* 3.0 27.4 + - + +
458B VAL* 4.1 19.7 - - + -
476B LEU* 3.9 30.7 - - + -
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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 GLY 3.0 18.8 + - - +
359B ASN* 3.9 11.0 - - - +
361B ALA* 1.3 75.0 - - - +
363B ARG* 1.3 61.1 + - + +
365B LEU* 4.8 2.5 - - - +
366B SER* 2.9 46.5 + - - -
479B LEU* 5.5 0.5 - - - +
505B PRO* 3.8 23.9 + - - +
506B SER* 3.2 34.0 + - - +
507B GLY* 3.7 7.1 + - - +
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Residues in contact with ARG 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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359B ASN* 2.8 32.5 + - + +
360B LEU* 4.4 4.0 - - - +
362B GLN* 1.3 75.2 - - + +
364B SER* 1.3 60.7 + - - +
366B SER* 3.9 5.3 - - - -
367B MET* 3.4 32.5 + - + +
424B ASN* 4.0 18.6 + - - +
427B PHE* 3.7 42.7 - - + +
428B SER* 4.5 12.5 + - - -
433B TRP* 4.2 15.4 - - - -
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 2.8 22.6 + - - -
361B ALA* 2.9 15.8 + - - -
363B ARG* 1.3 78.7 - - - +
365B LEU* 1.3 59.9 + - - +
367B MET 3.3 1.7 + - - -
368B VAL* 3.3 26.5 + - - +
427B PHE* 4.3 7.1 - - - -
451B LEU* 3.3 22.4 - - - +
454B THR* 3.9 23.6 - - - +
455B LEU* 3.8 15.1 - - - +
458B VAL* 4.8 2.3 - - - +
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Residues in contact with LEU 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 ALA* 3.0 33.8 + - + +
362B GLN* 4.2 2.9 - - - +
364B SER* 1.3 72.9 + - - +
366B SER* 1.3 60.4 + - - +
368B VAL* 3.4 5.9 + - - +
369B ALA* 3.1 28.1 + - - +
455B LEU* 3.8 22.4 - - + -
458B VAL* 5.9 0.4 - - + -
476B LEU* 4.7 5.4 - - + -
479B LEU* 3.4 55.9 - - + +
480B LEU* 4.3 9.6 - - + -
502B LEU* 3.9 16.8 - - + -
503B PRO 6.0 0.4 - - - +
505B PRO* 3.5 20.1 - - + +
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Residues in contact with SER 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 2.9 32.7 + - - -
363B ARG* 3.9 6.7 - - - -
365B LEU* 1.3 77.0 - - - +
367B MET* 1.3 58.6 + - - +
369B ALA* 3.3 2.7 + - - +
370B LYS* 3.1 52.4 + - - +
505B PRO* 4.1 9.3 - - - +
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Residues in contact with MET 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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363B ARG* 3.4 12.7 + - + +
364B SER 3.3 9.4 + - - +
366B SER* 1.3 75.6 - - - +
368B VAL* 1.3 61.3 + - - +
371B ASN* 2.9 41.4 + - - +
372B LEU* 3.5 4.9 + - - +
427B PHE* 4.1 28.5 - - + -
432B PRO* 4.2 6.3 - - + -
433B TRP* 3.8 31.4 - - + +
436B ARG* 3.5 28.9 - - - +
447B PHE* 4.1 25.8 - - + -
451B LEU* 4.3 9.2 - - + -
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER 3.3 16.7 + - - +
365B LEU* 3.7 9.4 - - - +
367B MET* 1.3 76.5 - - - +
369B ALA* 1.3 59.6 + - - +
372B LEU* 3.3 29.1 + - + -
373B GLY 3.3 0.7 + - - -
374B ALA* 3.0 20.8 + - - -
375B ALA 3.3 31.0 - - - +
377B PRO* 4.4 4.0 - - + -
451B LEU* 4.1 11.7 - - + -
455B LEU* 3.8 23.6 - - + -
502B LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 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 LEU 3.1 17.6 + - - +
366B SER* 3.3 5.1 + - - +
368B VAL* 1.3 78.1 - - - +
370B LYS* 1.3 64.5 + - + +
373B GLY* 4.4 2.9 + - - -
374B ALA* 3.9 25.4 + - + +
503B PRO 5.7 0.2 - - - +
504B ALA* 5.5 1.3 - - - -
505B PRO* 3.8 24.5 - - + -
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Residues in contact with LYS 370 (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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366B SER* 3.1 32.0 + - - +
367B MET* 5.1 0.2 - - - -
369B ALA* 1.3 84.7 - - + +
371B ASN* 1.3 71.6 + - - +
372B LEU 3.6 0.8 + - - -
373B GLY 4.7 2.2 + - - -
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Residues in contact with ASN 371 (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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367B MET* 2.9 25.7 + - - +
370B LYS* 1.3 86.2 + - - +
372B LEU* 1.3 66.9 + - - +
373B GLY 3.8 0.7 - - - -
436B ARG* 3.6 41.2 + - + +
447B PHE* 4.0 18.1 - - + -
448B ARG* 5.0 4.0 + - - -
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Residues in contact with LEU 372 (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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367B MET 3.5 1.5 + - - +
368B VAL* 3.3 32.6 + - + +
371B ASN* 1.3 85.9 - - - +
373B GLY* 1.3 63.6 + - - +
374B ALA 3.6 0.3 + - - -
375B ALA* 3.9 18.2 + - - +
377B PRO* 3.8 31.4 - - + -
447B PHE* 3.8 26.0 - - + -
448B ARG* 3.7 41.5 - - + +
451B LEU* 4.4 9.2 - - + -
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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