Contacts of the helix formed by residues 357 - 372 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ASP 3.3 10.2 + - - +
353C LEU* 3.7 7.4 - - + +
356C GLU* 1.3 78.2 - - - +
358C GLY* 1.3 66.9 + - - +
359C ASN 3.5 0.2 - - - -
360C LEU* 3.5 3.8 + - + +
361C ALA* 3.1 21.0 + - - +
417C TRP* 4.0 17.0 - - + -
420C LEU* 4.0 27.6 - - + -
458C VAL* 5.0 11.2 - - + -
461C ALA* 5.1 3.6 - - + -
462C SER* 5.3 1.3 - - - +
465C LEU* 3.9 27.1 - - + -
469C MET* 4.4 1.8 - - + -
473C THR* 6.3 0.4 - - + -
476C LEU* 4.4 16.8 - - + -
509C PHE* 3.6 33.4 - - + -
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Residues in contact with GLY 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU 2.7 22.4 + - - -
354C ALA* 3.4 10.0 + - - -
357C LEU* 1.3 74.2 - - - +
359C ASN* 1.3 57.8 + - - +
361C ALA* 3.5 4.5 + - - +
362C GLN* 3.0 29.5 + - - +
509C PHE* 4.4 18.4 - - - -
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Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C ALA 3.2 11.3 + - - +
355C ASN* 2.8 42.7 + - - +
358C GLY* 1.3 74.6 - - - +
360C LEU* 1.3 58.5 + - - +
362C GLN* 4.3 6.5 - - - +
363C ARG* 2.8 64.7 + - + +
424C ASN* 5.7 0.2 - - - +
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Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ASN 3.9 3.2 + - - -
356C GLU 3.4 17.3 - - - +
357C LEU* 3.5 3.8 + - + +
358C GLY 3.4 0.2 - - - -
359C ASN* 1.3 77.6 - - - +
361C ALA* 1.3 58.3 + - - +
363C ARG* 4.2 5.0 - - - +
364C SER* 2.8 28.1 + - - -
420C LEU* 3.9 28.3 - - + +
423C ALA* 3.8 24.0 - - + +
424C ASN* 3.4 34.2 + - - +
427C PHE* 4.5 9.4 - - + -
454C THR* 3.8 22.6 - - + +
457C VAL* 5.1 0.7 - - + -
458C VAL* 3.8 23.1 - - + -
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 3.1 17.3 + - + +
358C GLY* 3.8 5.2 - - - +
360C LEU* 1.3 77.6 - - - +
362C GLN* 1.3 57.5 + - - +
364C SER* 3.1 5.6 + - - -
365C LEU* 2.9 39.1 + - + +
458C VAL* 4.1 18.1 - - + +
476C LEU* 3.9 32.5 - - + -
508C ILE* 5.3 4.5 - - + -
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C GLY 3.0 18.9 + - - +
359C ASN* 4.0 7.9 - - - +
360C LEU 3.4 0.2 - - - -
361C ALA* 1.3 74.9 - - - +
363C ARG* 1.3 59.9 + - + +
365C LEU* 4.7 2.6 - - - +
366C SER* 2.9 42.7 + - - -
505C PRO* 4.1 26.8 + - - +
506C SER* 3.7 25.6 - - - +
507C GLY* 4.3 5.7 + - - -
508C ILE* 5.7 0.9 - - - +
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Residues in contact with ARG 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ASN* 5.0 4.0 + - - -
359C ASN* 2.8 51.9 + - - +
360C LEU* 4.2 4.3 - - - +
362C GLN* 1.3 74.6 - - + +
364C SER* 1.3 61.9 + - - +
366C SER* 3.7 5.4 - - - -
367C MET* 3.2 29.3 + - + +
424C ASN* 4.4 13.9 + - - -
427C PHE* 4.1 31.2 - - + -
428C SER* 5.8 1.4 + - - -
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Residues in contact with SER 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU 2.8 21.7 + - - -
361C ALA* 3.1 10.9 + - - -
363C ARG* 1.3 77.0 - - - +
365C LEU* 1.3 63.1 + - - +
367C MET 3.4 0.7 + - - -
368C VAL* 3.2 25.1 + - - +
427C PHE* 4.4 6.5 - - - -
451C LEU* 3.4 20.2 - - - +
454C THR* 3.9 24.5 - - - +
455C LEU* 3.9 18.1 - - - +
458C VAL* 4.6 3.8 - - - +
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Residues in contact with LEU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ALA* 2.9 29.8 + - + +
362C GLN* 4.2 4.3 - - - +
364C SER* 1.3 73.9 + - - +
366C SER* 1.3 61.5 + - - +
368C VAL* 3.4 6.6 + - - +
369C ALA* 3.1 26.9 + - - +
455C LEU* 3.8 15.9 - - + -
458C VAL* 6.2 0.4 - - + -
476C LEU* 4.2 15.9 - - + -
479C LEU* 3.6 52.3 - - + +
480C LEU* 4.1 10.8 - - + -
502C LEU* 3.8 19.3 - - + -
505C PRO* 3.6 19.8 - - + +
508C ILE* 5.2 1.1 - - + -
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Residues in contact with SER 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 2.9 31.5 + - - -
363C ARG* 3.7 7.2 - - - -
365C LEU* 1.3 77.2 - - - +
367C MET* 1.3 57.3 + - - +
369C ALA* 3.4 2.4 + - - +
370C LYS* 3.0 53.6 + - - +
505C PRO* 4.3 8.7 - - - +
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Residues in contact with MET 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ARG* 3.2 10.8 + - + +
364C SER 3.7 8.1 - - - +
365C LEU 3.3 0.2 - - - -
366C SER* 1.3 75.5 - - - +
368C VAL* 1.3 60.4 + - - +
371C ASN* 2.9 46.9 + - - +
372C LEU* 3.4 3.3 + - - +
427C PHE* 3.9 32.3 - - + -
432C PRO* 3.9 6.1 - - + -
433C TRP* 3.7 40.8 - - + +
436C ARG* 3.9 13.9 - - - +
447C PHE* 4.0 20.2 - - + -
451C LEU* 3.8 19.4 - - + +
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Residues in contact with VAL 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER 3.2 16.3 + - - +
365C LEU* 3.6 9.2 - - - +
366C SER 3.3 0.2 - - - -
367C MET* 1.3 77.6 - - - +
369C ALA* 1.3 60.8 + - - +
372C LEU* 3.2 18.7 + - - -
374C ALA* 2.9 23.2 + - - -
375C ALA 3.4 30.3 - - - +
377C PRO* 4.3 5.2 - - + -
451C LEU* 3.9 10.8 - - + -
455C LEU* 3.7 31.9 - - + -
502C LEU* 3.6 24.5 - - + -
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Residues in contact with ALA 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C LEU 3.1 16.4 + - - +
366C SER* 3.4 4.7 + - - +
368C VAL* 1.3 79.3 - - - +
370C LYS* 1.3 62.3 + - + +
373C GLY* 4.5 3.8 + - - -
374C ALA* 4.0 21.9 + - + +
504C ALA* 5.6 1.3 - - - -
505C PRO* 3.9 24.0 - - + -
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Residues in contact with LYS 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C SER* 3.0 32.9 + - - +
367C MET* 4.9 0.2 - - - -
369C ALA* 1.3 82.9 - - + +
371C ASN* 1.3 73.3 + - - +
372C LEU 3.8 0.2 - - - -
373C GLY* 4.9 1.3 - - - -
436C ARG* 5.1 7.0 - - - +
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Residues in contact with ASN 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C MET* 2.9 25.2 + - - +
370C LYS* 1.3 86.1 + - - +
372C LEU* 1.3 67.1 + - - +
373C GLY 3.6 1.6 - - - -
436C ARG* 2.7 51.3 + - + +
447C PHE* 3.9 18.8 - - + -
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C MET 3.4 0.6 + - - +
368C VAL* 3.2 14.2 + - - +
371C ASN* 1.3 81.6 - - + +
373C GLY* 1.3 63.8 + - - +
374C ALA 3.3 2.0 - - - -
375C ALA* 3.3 29.5 + - + +
377C PRO* 3.9 33.4 - - + -
447C PHE* 3.4 35.4 - - + -
448C ARG* 4.9 11.4 - - + -
451C LEU* 3.8 15.3 - - + -
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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