Contacts of the helix formed by residues 357 - 372 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ASP 3.2 13.6 + - - +
353A LEU* 3.8 4.0 - - + +
356A GLU* 1.3 77.6 - - - +
358A GLY* 1.3 66.5 + - - +
359A ASN 3.5 0.2 - - - -
360A LEU* 3.6 3.5 + - + +
361A ALA* 3.1 26.5 + - - +
417A TRP* 4.0 25.6 - - + -
420A LEU* 3.9 28.3 - - + -
458A VAL* 5.4 8.1 - - + -
461A ALA* 5.0 4.7 - - + -
462A SER* 5.3 1.8 - - - +
465A LEU* 4.0 17.7 - - + -
469A MET* 4.1 2.9 - - + -
473A THR* 6.4 0.7 - - + -
476A LEU* 4.4 16.8 - - + -
509A PHE* 3.7 34.1 - - + -
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Residues in contact with GLY 358 (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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353A LEU 2.7 23.0 + - - -
354A ALA 3.5 6.0 + - - -
357A LEU* 1.3 73.1 - - - +
359A ASN* 1.3 57.3 + - - +
361A ALA* 3.4 6.1 + - - +
362A GLN* 2.9 30.1 + - - +
508A ILE 6.0 1.1 - - - -
509A PHE* 4.1 20.2 - - - -
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Residues in contact with ASN 359 (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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354A ALA 3.1 12.6 + - - +
355A ASN* 3.1 35.0 + - - +
358A GLY* 1.3 71.7 - - - +
360A LEU* 1.3 59.5 + - - +
362A GLN* 4.4 6.7 - - - +
363A ARG* 2.8 52.2 + - - +
424A ASN* 5.4 3.2 + - - -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASN 3.8 2.8 + - - -
356A GLU 3.4 22.0 - - - +
357A LEU 3.6 3.7 + - - +
358A GLY 3.4 0.2 - - - -
359A ASN* 1.3 79.4 - - - +
361A ALA* 1.3 59.0 + - - +
363A ARG* 4.3 3.7 - - - +
364A SER* 2.8 28.1 + - - -
420A LEU* 4.1 20.4 - - + +
423A ALA* 3.8 40.2 - - + +
424A ASN* 3.4 27.1 + - - +
427A PHE* 4.4 11.3 - - + -
454A THR* 4.0 15.3 - - + -
458A VAL* 4.1 17.9 - - + -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.1 20.1 + - + +
358A GLY* 3.7 4.5 - - - +
360A LEU* 1.3 76.2 - - - +
362A GLN* 1.3 59.3 + - - +
364A SER* 3.0 16.9 + - - -
365A LEU* 3.1 26.3 + - + +
458A VAL* 4.2 19.1 - - + -
476A LEU* 3.9 31.6 - - + -
508A ILE* 6.1 0.4 - - + -
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Residues in contact with GLN 362 (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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358A GLY 2.9 18.2 + - - +
359A ASN* 3.3 8.5 + - - +
361A ALA* 1.3 74.1 - - - +
363A ARG* 1.3 61.3 + - + +
365A LEU* 4.8 2.3 - - - +
366A SER* 2.9 49.7 + - - -
479A LEU* 5.6 0.7 - - - +
505A PRO* 4.1 19.9 + - - +
506A SER* 3.3 29.0 + - - +
507A GLY* 3.4 13.0 + - - +
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Residues in contact with ARG 363 (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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359A ASN* 2.8 48.0 + - - +
360A LEU* 4.3 3.6 - - - +
362A GLN* 1.3 73.5 - - + +
364A SER* 1.3 59.6 + - - +
366A SER* 3.1 16.8 + - - -
367A MET* 3.4 35.3 - - - +
427A PHE* 4.2 24.4 - - + -
433A TRP* 3.4 42.8 - - - +
436A ARG* 5.3 3.6 - - - +
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU 2.8 21.5 + - - -
361A ALA* 3.0 9.7 + - - -
363A ARG* 1.3 78.2 - - - +
365A LEU* 1.3 65.6 + - - +
367A MET 3.4 1.2 + - - -
368A VAL* 3.3 14.6 + - - +
427A PHE* 4.3 6.3 - - - -
451A LEU* 3.3 30.1 - - - +
454A THR* 3.8 24.2 - - - +
455A LEU* 3.6 20.0 - - - +
458A VAL* 4.7 2.9 - - - +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ALA* 3.1 23.5 + - + +
362A GLN* 4.2 2.5 - - - +
364A SER* 1.3 78.0 + - - +
366A SER* 1.3 59.2 + - - +
368A VAL* 3.4 6.3 + - - +
369A ALA* 3.1 22.2 + - - +
455A LEU* 3.8 21.8 - - + -
458A VAL* 5.9 0.7 - - + -
476A LEU* 4.4 13.5 - - + -
479A LEU* 3.6 53.2 - - + +
480A LEU* 4.0 11.0 - - + -
502A LEU* 3.9 18.3 - - + +
505A PRO* 3.6 23.9 - - + +
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLN* 2.9 35.8 + - - +
363A ARG* 3.1 12.5 + - - -
365A LEU* 1.3 74.6 - - - +
367A MET* 1.3 65.0 + - - +
369A ALA* 3.4 1.9 + - - +
370A LYS* 3.0 53.0 + - - +
505A PRO* 4.2 9.6 - - - +
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Residues in contact with MET 367 (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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363A ARG* 3.4 28.2 + - - +
364A SER 3.4 6.7 + - - +
365A LEU 3.3 0.2 - - - -
366A SER* 1.3 81.9 + - - +
368A VAL* 1.3 58.0 + - - +
370A LYS* 5.0 0.4 - - - -
371A ASN* 2.9 39.3 + - - +
372A LEU* 3.5 5.3 + - - +
427A PHE* 4.0 24.2 - - + -
432A PRO* 4.0 20.4 - - + -
433A TRP* 3.9 30.5 - - + +
436A ARG* 3.7 29.2 - - - +
447A PHE* 4.1 15.4 - - + -
451A LEU* 4.0 9.6 - - + -
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER 3.3 14.5 + - - +
365A LEU* 3.6 10.3 - - - +
366A SER 3.2 0.4 - - - -
367A MET* 1.3 77.6 - - - +
369A ALA* 1.3 58.1 + - - +
372A LEU* 3.1 32.4 + - + -
374A ALA* 3.0 18.7 + - - -
375A ALA 3.4 34.8 - - - +
376A VAL 4.5 0.2 - - - +
377A PRO* 4.3 4.0 - - + -
451A LEU* 4.1 11.2 - - + -
455A LEU* 3.8 25.1 - - + -
502A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU 3.1 16.8 + - - +
366A SER* 3.4 4.0 + - - +
368A VAL* 1.3 77.3 - - - +
370A LYS* 1.3 63.4 + - + +
373A GLY* 4.7 2.6 + - - -
374A ALA* 3.8 27.6 + - + +
503A PRO 5.5 1.1 - - - +
504A ALA* 5.4 1.6 - - - -
505A PRO* 3.7 25.4 - - + -
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Residues in contact with LYS 370 (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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366A SER* 3.0 33.6 + - - +
367A MET* 5.7 0.2 - - - -
369A ALA* 1.3 83.1 - - + +
371A ASN* 1.3 73.6 + - - +
372A LEU 3.7 0.4 - - - -
373A GLY* 4.8 2.4 + - - -
436A ARG* 6.2 2.2 - - - +
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Residues in contact with ASN 371 (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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367A MET* 2.9 23.4 + - - +
370A LYS* 1.3 89.2 + - - +
372A LEU* 1.3 66.0 + - - +
373A GLY 3.7 1.7 + - - -
436A ARG* 3.0 45.0 + - + +
447A PHE* 4.3 15.8 - - + -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MET 3.5 1.3 + - - +
368A VAL* 3.1 26.1 + - + +
371A ASN* 1.3 83.0 - - - +
373A GLY* 1.3 64.1 + - - +
374A ALA 3.4 0.3 + - - -
375A ALA* 3.7 18.7 + - - +
377A PRO* 3.8 30.1 - - + -
444A GLN* 6.0 1.6 - - - +
447A PHE* 3.7 33.9 - - + -
448A ARG* 3.9 24.9 - - + -
451A LEU* 4.2 15.5 - - + -
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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