Contacts of the helix formed by residues 342 - 360 (chain C) in PDB entry 2GPV
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 342 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LEU* 3.9 12.6 - - + -
268C LEU* 3.8 29.2 - - + -
332C MET* 4.4 8.7 - - + -
337C SER* 3.1 7.8 + - - +
340C ALA* 3.8 24.2 - - + +
341C GLY* 1.3 78.9 - - - +
343C LEU* 1.3 54.5 + - - +
344C ASP 3.4 2.2 - - - -
345C LEU* 3.9 14.6 - - + -
346C ASN* 2.7 54.9 + - - +
434C HIS* 3.6 22.9 - - + +
502C OHT 3.5 30.5 - - + -
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C GLU* 4.2 22.0 - - + +
337C SER* 3.5 26.0 + - - +
338C LYS* 3.6 36.6 - - + +
341C GLY* 3.3 4.9 + - - -
342C LEU* 1.3 76.5 - - - +
344C ASP* 1.3 67.7 + - - +
346C ASN* 4.1 0.3 - - - +
347C ASN* 2.9 56.0 + - - +
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Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLY 5.1 1.0 + - - -
342C LEU 3.4 0.2 - - - -
343C LEU* 1.3 86.8 - - - +
345C LEU* 1.3 61.5 + - - +
347C ASN* 3.8 9.1 + - - +
348C ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 3.4 20.5 + - + +
344C ASP* 1.3 75.9 - - - +
346C ASN* 1.3 59.9 + - - +
348C ALA* 3.1 8.9 + - + +
349C ILE* 2.9 34.0 + - + +
427C THR* 4.4 8.3 - - + +
430C LYS* 4.2 13.0 - - + +
431C ALA* 3.8 28.9 - - + +
434C HIS* 3.8 32.8 - - + +
502C OHT 3.6 41.5 - - + -
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Residues in contact with ASN 346 (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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324C LEU* 3.6 17.5 - - + +
326C TYR* 2.5 26.4 + - - -
332C MET* 3.7 24.9 + - - +
337C SER* 2.7 31.4 + - - +
342C LEU* 2.7 33.6 + - - +
343C LEU 4.1 1.3 - - - +
345C LEU* 1.3 74.4 - - - +
347C ASN* 1.3 58.0 + - - +
349C ILE* 3.3 8.3 + - - +
350C LEU* 2.9 34.3 + - + +
502C OHT 4.4 3.3 - - - +
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Residues in contact with ASN 347 (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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334C GLU* 5.3 6.7 + - - +
343C LEU* 2.9 44.3 + - - +
344C ASP* 3.8 9.4 + - - +
346C ASN* 1.3 73.2 - - - +
348C ALA* 1.3 66.3 + - - +
350C LEU* 3.1 23.5 + - - +
351C GLN* 3.0 21.1 + - - +
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Residues in contact with ALA 348 (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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344C ASP 2.9 16.2 + - - +
345C LEU* 3.3 14.4 - - + +
347C ASN* 1.3 76.7 - - - +
349C ILE* 1.3 61.5 + - - +
351C GLN* 3.1 27.8 + - - +
352C LEU* 3.5 4.5 + - - +
423C LEU* 5.4 0.5 - - - +
426C GLN* 6.3 0.4 - - - +
427C THR* 4.1 24.9 + - + +
430C LYS* 5.1 14.1 - - + -
380F MET* 6.4 3.4 - - - -
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Residues in contact with ILE 349 (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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310C ILE* 4.3 16.2 - - + -
313C VAL* 4.4 10.1 - - + -
314C VAL* 3.5 22.7 - - + -
324C LEU* 3.7 22.0 - - + -
326C TYR* 3.7 14.4 - - + +
345C LEU* 2.9 21.2 + - + +
346C ASN* 3.5 10.1 - - - +
348C ALA* 1.3 73.4 - - - +
350C LEU* 1.3 61.1 + - - +
352C LEU* 3.0 21.5 + - - +
353C VAL* 3.2 10.9 + - - +
427C THR* 3.9 19.1 - - + -
502C OHT 3.7 30.7 - - + -
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ASP* 3.9 44.4 - - + +
323C GLU 4.1 8.3 - - - +
324C LEU* 4.3 19.5 - - + -
346C ASN* 2.9 18.2 + - + +
347C ASN* 3.1 29.8 + - - +
349C ILE* 1.3 73.2 - - - +
351C GLN* 1.3 60.9 + - - +
353C VAL* 3.1 16.1 + - + +
354C LYS* 2.8 30.2 + - - +
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Residues in contact with GLN 351 (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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347C ASN 3.0 10.1 + - - +
348C ALA* 3.1 19.5 + - - +
350C LEU* 1.3 76.5 - - - +
352C LEU* 1.3 60.2 + - - +
354C LYS* 3.4 12.0 + - + +
355C LYS* 3.2 22.6 + - - +
423C LEU* 3.9 31.1 - - + +
426C GLN* 4.9 3.3 + - - -
378F ASP* 3.2 25.3 + - - +
379F SER 3.3 18.4 + - - -
380F MET* 3.7 20.9 + - - +
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Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ILE* 4.1 13.0 - - + -
311C LEU* 5.5 0.2 - - + -
314C VAL* 3.9 11.4 - - + -
348C ALA 3.5 2.1 + - - +
349C ILE* 3.0 12.0 + - - +
351C GLN* 1.3 76.7 - - - +
353C VAL* 1.3 64.9 + - - +
355C LYS* 3.6 6.7 + - + +
356C TYR* 3.2 61.7 + - + +
420C THR* 4.8 5.4 - - - +
423C LEU* 4.4 20.6 - - + +
424C LEU* 3.9 39.0 - - + +
427C THR* 3.9 27.4 - - + +
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Residues in contact with VAL 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C VAL* 4.1 19.7 - - + +
317C SER* 4.0 32.8 - - - +
318C LEU* 3.9 14.6 - - + -
320C PHE 5.1 0.7 - - - +
324C LEU* 4.3 7.0 - - + -
349C ILE 3.6 11.0 - - - +
350C LEU* 3.1 20.1 + - + +
352C LEU* 1.3 74.8 - - - +
354C LYS* 1.3 67.9 + - - +
355C LYS 3.0 0.9 + - - -
356C TYR* 3.1 2.6 + - - +
357C LYS* 2.8 52.0 + - + +
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU 2.8 15.9 + - - +
351C GLN* 3.6 15.7 - - + +
353C VAL* 1.3 73.1 - - - +
355C LYS* 1.3 64.8 + - - +
357C LYS* 3.3 10.4 + - - +
358C SER* 2.9 26.2 + - - +
385F VAL* 4.7 26.2 - - - +
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Residues in contact with LYS 355 (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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351C GLN* 3.2 11.6 + - - +
352C LEU* 3.9 8.5 - - + +
353C VAL 3.1 0.8 - - - -
354C LYS* 1.3 79.5 - - - +
356C TYR* 1.3 59.5 + - + +
358C SER* 2.9 29.6 + - - -
359C MET* 3.3 13.6 + - - +
419C MET 4.3 1.0 + - - -
420C THR* 3.8 36.0 - - + +
423C LEU* 4.0 18.0 - - - +
376F ASN* 4.2 11.1 + - - +
378F ASP* 2.6 39.3 + - - -
389F GLN* 4.6 17.5 - - - +
392F GLN* 5.9 3.1 - - - +
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Residues in contact with TYR 356 (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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311C LEU* 4.0 21.8 - - + +
314C VAL* 3.8 14.4 - - + -
318C LEU* 3.8 16.2 - - + -
352C LEU* 3.2 41.3 + - + +
353C VAL 3.1 2.0 + - - -
355C LYS* 1.3 76.6 - - + +
357C LYS* 1.3 60.2 + - - +
359C MET* 3.0 13.2 + - - +
360C LYS 2.8 24.6 + - - -
361C LEU* 3.2 37.4 + - + -
369C LEU* 3.4 25.9 - - + +
417C MET* 4.5 5.2 - - - -
420C THR* 2.7 47.5 + - + -
421C LEU* 5.4 0.7 - - - +
424C LEU* 5.0 6.4 - - - +
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Residues in contact with LYS 357 (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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318C LEU* 3.2 35.5 - - + +
319C SER 5.4 0.4 - - - -
320C PHE 2.9 20.2 + - - +
321C GLU* 2.7 37.5 + - - +
322C ASP* 5.0 2.4 + - - +
353C VAL* 2.8 35.6 + - + +
354C LYS* 3.4 14.1 - - - +
356C TYR* 1.3 71.6 - - - +
358C SER* 1.3 62.3 + - - +
360C LYS* 3.2 19.7 + - - +
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Residues in contact with SER 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LYS* 2.9 20.0 + - - +
355C LYS* 2.9 13.6 + - - -
357C LYS* 1.3 77.1 - - - +
359C MET* 1.3 60.9 + - - +
360C LYS* 3.4 6.6 - - - +
389F GLN* 5.1 12.8 + - - -
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Residues in contact with MET 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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355C LYS* 3.3 19.0 + - + +
356C TYR* 3.0 15.0 + - - +
358C SER* 1.3 79.1 - - - +
360C LYS* 1.3 66.1 + - - +
413C ARG* 2.9 41.3 + - + +
416C LYS* 4.1 20.6 - - + +
417C MET* 3.2 55.4 - - + +
420C THR* 4.2 20.2 - - - -
389F GLN* 6.0 3.4 - - - +
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Residues in contact with LYS 360 (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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318C LEU* 5.5 0.2 - - - -
356C TYR 2.8 7.7 + - - -
357C LYS* 3.2 13.9 + - - +
358C SER 4.7 5.6 - - - +
359C MET* 1.3 82.8 - - - +
361C LEU* 1.3 64.1 + - - +
362C GLU* 3.2 14.8 + - - +
413C ARG* 3.5 5.9 + - - -
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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