Contacts of the helix formed by residues 493 - 511 (chain C) in PDB entry 2V4M
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 THR 493 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C MET* 4.1 20.4 - - + -
346C GLU* 3.4 24.8 + - - +
347C ILE* 3.7 30.7 - - + -
350C GLN* 3.4 8.8 - - - +
487C GLU* 2.7 14.6 + - - -
491C ALA 3.4 11.1 + - - +
492C SER* 1.3 80.1 + - - +
494C LYS* 1.3 70.5 + - - -
495C ALA 3.2 0.2 - - - -
496C TYR* 3.1 21.2 + - - +
497C THR 3.4 4.3 + - - -
576C LYS* 4.5 1.8 - - - -
672C GLN* 3.6 19.8 + - + +
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LYS* 4.7 1.2 - - - +
346C GLU* 3.8 27.3 - - + +
349C GLU* 2.9 35.4 + - - +
350C GLN* 3.7 6.0 + - + -
353C SER* 3.6 17.9 - - - +
484C ALA* 2.8 33.1 + - + +
485C GLY* 3.5 12.2 - - - -
486C PRO* 2.7 32.0 + - - +
487C GLU* 3.7 11.7 - - + +
493C THR* 1.3 82.5 + - - +
495C ALA* 1.3 59.9 + - - +
497C THR* 3.2 10.0 + - - -
498C SER* 3.0 33.0 + - - -
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Residues in contact with ALA 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLN* 3.4 36.6 - - + -
466C ASN* 5.2 2.0 - - + +
482C ILE* 3.7 14.7 - - + +
484C ALA* 4.7 2.0 - - - -
487C GLU* 3.2 17.5 + - + +
492C SER* 3.7 6.1 - - - +
493C THR 3.2 0.8 - - - -
494C LYS* 1.3 79.1 - - + +
496C TYR* 1.3 58.1 + - - +
498C SER* 4.6 0.2 - - - -
499C GLN* 2.9 40.3 + - - +
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Residues in contact with TYR 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C THR* 3.7 35.9 - - + -
397C HIS* 3.7 10.3 - - + -
398C ALA* 3.5 28.6 - - + +
401C ALA* 3.5 22.3 - - + +
492C SER* 3.4 4.2 + - - +
493C THR* 3.1 11.7 + - - +
495C ALA* 1.3 78.8 - - - +
497C THR* 1.3 69.5 + - + +
499C GLN* 3.4 10.1 + - - +
500C PHE* 2.9 40.6 + + - +
568C ALA* 3.8 17.7 + - - +
569C THR* 4.5 3.1 + - - -
572C GLU* 4.2 14.7 - - + +
664C GLY 5.0 3.4 + - - -
668C VAL* 4.1 29.6 - - + +
672C GLN* 4.7 3.6 - - - +
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Residues in contact with THR 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C GLN* 2.7 38.0 + - + +
353C SER* 5.0 0.7 + - - -
354C VAL* 4.5 10.7 - - - +
493C THR 3.4 0.8 + - - +
494C LYS* 3.2 13.5 + - - +
496C TYR* 1.3 93.4 - - + +
498C SER* 1.3 57.2 + - - +
500C PHE* 3.3 8.2 - - - +
501C VAL* 3.0 34.1 + - - +
665C ILE* 3.8 31.5 - - + +
668C VAL* 4.5 12.8 - - + -
669C ILE* 5.0 0.7 - - + -
672C GLN* 4.6 0.4 - - - +
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Residues in contact with SER 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C SER* 3.7 15.6 + - - -
354C VAL* 4.3 2.5 + - - +
357C THR* 2.9 28.8 + - - +
482C ILE* 3.9 18.2 - - - -
484C ALA* 3.7 11.6 - - - +
494C LYS 3.0 18.9 + - - -
497C THR* 1.3 75.7 + - - +
499C GLN* 1.3 56.1 + - - +
501C VAL* 4.4 4.7 - - - +
502C SER* 2.7 38.3 + - - -
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Residues in contact with GLN 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C THR* 4.7 1.4 - - - +
395C SER* 2.9 45.2 + - - -
398C ALA* 3.8 13.8 - - + +
438C LEU* 4.1 4.6 - - + +
439C SER 3.7 17.2 - - - +
440C GLN* 3.8 12.3 - - - +
464C ILE* 4.4 11.4 + - + +
482C ILE* 4.0 18.5 - - + +
492C SER* 5.2 0.3 + - - -
495C ALA* 2.9 29.2 + - - +
496C TYR* 3.5 13.9 - - - +
498C SER* 1.3 73.9 - - - +
500C PHE* 1.3 57.9 + - - +
502C SER* 3.2 7.1 + - - -
503C LEU* 2.9 38.1 + - + +
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Residues in contact with PHE 500 (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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398C ALA* 4.5 6.7 - - + +
401C ALA* 3.7 36.1 - - + -
402C THR* 3.4 19.0 - - + +
496C TYR* 2.9 26.8 + + - +
497C THR* 3.3 12.3 - - - +
499C GLN* 1.3 74.7 - - - +
501C VAL* 1.3 64.4 + - - +
503C LEU 3.1 3.1 + - - -
504C VAL* 2.9 31.7 + - + +
565C TYR* 5.9 1.8 - + - -
661C CYS 3.3 28.7 - - - -
662C LEU* 4.3 5.4 - - + -
664C GLY* 4.1 10.5 - - - -
665C ILE* 3.7 45.8 - - + -
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Residues in contact with VAL 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 4.2 21.8 - - + +
357C THR* 3.9 13.2 - - + -
358C MET* 3.8 28.9 - - + -
497C THR 3.0 18.5 + - - +
498C SER* 3.9 4.5 - - - +
500C PHE* 1.3 75.7 - - - +
502C SER* 1.3 63.6 + - - +
504C VAL* 3.2 8.7 + - - +
505C MET* 3.0 27.3 + - + +
528C LEU* 3.8 21.3 - - + -
531C LEU* 4.4 0.2 - - + -
665C ILE* 3.7 19.5 - - + -
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Residues in contact with SER 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C THR* 3.5 12.3 - - - +
371C LEU* 4.5 3.6 - - - +
464C ILE* 4.2 12.7 - - - +
480C VAL* 4.5 11.7 - - - +
482C ILE* 3.3 26.8 - - - +
498C SER 2.7 28.0 + - - -
499C GLN 3.2 5.3 + - - -
501C VAL* 1.3 73.4 - - - +
503C LEU* 1.3 58.3 + - - +
505C MET* 3.3 15.9 + - - +
506C PHE* 3.0 26.2 + - - +
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU* 4.7 6.1 - - + -
398C ALA* 3.8 11.7 - - + +
399C GLY* 4.4 1.6 - - - +
402C THR* 3.2 32.5 - - + +
406C LEU* 3.9 20.9 - - + +
436C PHE* 4.4 20.9 - - + -
438C LEU* 3.9 39.5 - - + -
464C ILE* 4.6 10.1 - - + -
499C GLN* 2.9 21.3 + - + +
500C PHE 3.1 5.1 + - - +
502C SER* 1.3 72.8 - - - +
504C VAL* 1.3 65.8 + - - +
506C PHE* 3.3 7.6 + - + +
507C ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 504 (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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402C THR* 4.1 7.2 - - + -
405C VAL* 4.3 14.6 - - + -
500C PHE* 2.9 42.4 + - + +
501C VAL* 3.2 9.4 + - - +
503C LEU* 1.3 76.6 - - - +
505C MET* 1.3 55.9 + - - +
507C ALA* 3.1 9.3 + - - +
508C LEU* 3.0 33.6 + - + +
524C ILE* 3.7 31.9 - - + -
528C LEU* 4.4 6.7 - - + -
661C CYS* 4.3 4.9 - - - +
662C LEU* 4.1 14.8 - - + -
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Residues in contact with MET 505 (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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357C THR* 3.5 36.6 - - + +
358C MET* 4.1 9.0 - - - -
361C ARG* 4.0 26.5 - - - +
362C VAL* 3.6 31.4 - - + -
369C VAL* 3.4 25.4 - - + +
371C LEU* 4.0 12.1 - - + -
501C VAL* 3.0 18.1 + - + +
502C SER* 3.7 18.8 - - - +
504C VAL* 1.3 72.7 - - - +
506C PHE* 1.3 66.6 + - - +
508C LEU* 3.3 7.1 + - - +
509C MET* 3.0 19.9 + - - +
528C LEU* 4.4 8.5 - - + -
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Residues in contact with PHE 506 (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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371C LEU* 3.7 12.4 - - + +
374C LEU* 3.6 27.1 - - + -
378C ILE* 4.6 6.1 - - + -
381C ILE* 3.6 22.9 - - + -
387C LEU* 3.8 20.4 - - + -
406C LEU* 3.8 15.3 - - + -
410C THR* 4.6 0.7 - - + -
436C PHE* 3.5 40.8 - + + -
464C ILE* 6.0 2.7 - - + -
480C VAL* 6.1 0.7 - - + -
502C SER 3.0 13.7 + - - +
503C LEU* 3.6 11.7 - - + +
505C MET* 1.3 76.6 - - - +
507C ALA* 1.3 62.8 + - - +
509C MET* 3.2 6.8 + - + +
510C MET* 3.1 57.0 + - + +
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Residues in contact with ALA 507 (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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405C VAL* 4.2 14.4 - - + +
406C LEU* 3.8 21.3 - - + -
409C LEU* 3.6 24.3 - - + +
410C THR* 4.9 1.8 - - - -
503C LEU 3.0 13.0 + - - +
504C VAL* 3.1 13.0 + - - +
506C PHE* 1.3 78.3 - - - +
508C LEU* 1.3 60.4 + - - +
510C MET* 3.3 14.9 + - - +
511C CYS* 3.4 15.9 + - - -
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Residues in contact with LEU 508 (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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369C VAL* 3.9 14.8 - - + -
409C LEU* 4.0 16.8 - - + -
504C VAL* 3.0 36.8 + - + +
505C MET* 3.8 4.7 - - - +
506C PHE 3.3 0.4 - - - -
507C ALA* 1.3 73.0 - - - +
509C MET* 1.3 64.7 + - - +
510C MET 3.4 0.3 + - - -
511C CYS* 3.5 3.3 - - - -
521C ARG* 2.2 73.6 + - + +
524C ILE* 4.0 18.8 - - + -
525C MET* 3.7 31.2 - - + -
528C LEU* 4.1 4.3 - - + -
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Residues in contact with MET 509 (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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369C VAL* 3.8 19.9 - - + +
370C ASN* 4.0 12.3 - - - +
371C LEU* 3.4 57.2 - - - +
374C LEU* 4.6 6.7 - - + +
375C LYS* 5.9 1.3 - - - -
378C ILE* 3.9 39.9 - - + -
382C GLN* 3.9 5.4 + - - +
505C MET 3.0 13.1 + - - +
506C PHE* 3.3 11.0 - - + +
508C LEU* 1.3 78.2 - - - +
510C MET* 1.3 60.8 + - - +
512C ASP* 3.3 28.9 - - - +
521C ARG* 5.6 0.2 - - - +
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Residues in contact with MET 510 (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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378C ILE* 4.6 3.6 - - - -
381C ILE* 3.9 27.6 - - + +
382C GLN* 3.9 35.0 + - + +
384C CYS* 5.2 0.9 - - - -
387C LEU* 5.4 0.9 - - + -
409C LEU 4.6 1.8 - - - -
410C THR* 3.7 36.3 - - + +
412C LEU* 4.5 11.9 - - + -
506C PHE* 3.1 52.6 + - + +
507C ALA 3.6 8.1 - - - +
508C LEU 3.2 0.8 - - - -
509C MET* 1.3 78.2 - - + +
511C CYS* 1.3 57.1 + - - +
512C ASP* 3.3 7.5 + - - +
513C ASP* 4.9 1.0 + - - +
514C ARG* 4.4 6.3 + - - -
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Residues in contact with CYS 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LEU* 3.3 39.0 - - + +
507C ALA 3.4 9.2 + - - -
508C LEU* 3.5 7.4 - - - -
509C MET 3.5 0.2 - - - -
510C MET* 1.3 76.0 - - - +
512C ASP* 1.3 54.9 + - - +
513C ASP 3.1 10.8 + - - -
514C ARG* 3.3 21.3 + - - +
517C MET* 3.5 17.3 - - - -
521C ARG* 3.2 44.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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