Contacts of the helix formed by residues 555 - 574 (chain B) in PDB entry 6QVC
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 HIS 555 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B PHE* 5.1 16.8 - + - +
342B PRO* 4.7 14.9 - - + +
343B PHE* 3.2 37.0 - + + -
351B PHE* 4.4 12.8 - + - -
520B LEU* 6.0 4.0 - - + +
523B GLY* 3.5 30.5 + - - -
524B TYR* 6.4 1.3 - + - -
526B VAL* 4.9 6.1 - - + -
527B ILE* 3.7 21.2 - - + +
552B GLN 5.2 0.8 + - - -
553B ILE* 3.5 1.2 - - - +
554B ALA* 1.3 85.4 - - + +
556B ILE* 1.3 58.9 + - - -
558B PRO* 3.6 7.2 - - + -
559B MET* 3.3 34.1 + - + +
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Residues in contact with ILE 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.6 0.9 - - + -
331A ALA* 6.3 2.7 - - + -
548A GLU* 4.2 20.0 - - + +
547B PHE* 3.5 45.8 - - + -
553B ILE* 3.2 33.2 - - + +
554B ALA 2.9 13.6 + - - +
555B HIS* 1.3 70.5 - - - +
557B LEU* 1.3 76.7 + - + +
558B PRO* 3.7 0.6 - - - +
559B MET* 3.2 10.6 - - + +
560B MET* 3.0 50.8 + - + +
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Residues in contact with LEU 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 6.0 4.5 - - + -
310A THR* 4.6 5.8 + - - +
313A ALA* 4.5 8.1 - - + +
314A PHE* 3.9 45.5 - - + +
317A ARG* 4.8 4.5 - - + -
329A ILE* 3.7 42.8 - - + +
330A THR 6.3 0.2 - - - -
331A ALA* 6.6 0.4 - - - -
343B PHE* 5.2 0.7 - - + -
554B ALA 4.9 2.2 - - - +
556B ILE* 1.3 94.2 - - + +
558B PRO* 1.3 72.2 - - + +
560B MET* 3.3 11.3 + - - +
561B VAL* 3.0 33.7 + - - +
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Residues in contact with PRO 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 6.4 1.8 - - + -
329A ILE* 5.7 4.7 - - + -
343B PHE* 3.6 27.8 - - + -
348B LEU* 4.6 11.9 - - + -
351B PHE* 3.6 33.8 - - + +
527B ILE* 5.2 3.5 - - + +
555B HIS* 3.6 17.0 - - + +
556B ILE 3.7 0.7 - - - +
557B LEU* 1.3 100.2 - - + +
559B MET* 1.3 56.5 + - - +
561B VAL* 3.4 7.2 + - + +
562B ALA* 2.9 30.0 + - - +
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Residues in contact with MET 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B VAL* 4.9 10.5 - - + -
527B ILE* 3.7 33.3 - - + +
530B ALA* 4.4 16.6 - - + -
543B ALA* 3.8 27.8 - - + +
546B CYS* 4.6 4.7 - - - -
547B PHE* 4.0 29.8 - - + +
550B THR* 5.3 3.4 - - + -
552B GLN 5.6 1.6 - - - +
553B ILE* 6.1 0.4 - - - -
555B HIS* 3.3 31.6 + - + +
556B ILE* 3.2 19.7 - - + +
557B LEU 3.3 0.2 - - - -
558B PRO* 1.3 78.4 - - - +
560B MET* 1.3 60.1 + - + +
562B ALA* 4.0 3.3 - - - +
563B VAL* 2.9 34.3 + - - +
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Residues in contact with MET 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 4.0 24.9 - - - -
283A LEU* 3.8 39.7 - - + +
306A PHE* 4.3 22.0 - - + -
310A THR* 3.8 14.8 - - - +
548A GLU* 4.5 3.1 - - - +
543B ALA* 5.1 9.0 - - + -
544B VAL* 5.8 1.6 - - + -
547B PHE* 4.6 4.0 - - + -
556B ILE* 3.0 48.1 + - + +
557B LEU* 3.7 6.5 - - - +
558B PRO 3.3 0.2 - - - -
559B MET* 1.3 80.8 - - + +
561B VAL* 1.3 61.8 + - - +
563B VAL* 3.4 5.7 + - - +
564B ILE* 3.0 32.7 + - - +
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Residues in contact with VAL 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 4.4 15.5 - - + +
311A PHE* 6.1 4.5 - - + -
314A PHE* 4.7 26.9 - - + -
348B LEU* 6.6 0.2 - - + -
557B LEU 3.0 22.6 + - - +
558B PRO* 3.7 7.0 - - + +
560B MET* 1.3 76.7 - - - +
562B ALA* 1.3 59.0 + - - +
564B ILE* 3.2 6.4 + - - +
565B LEU* 2.9 45.7 + - + +
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Residues in contact with ALA 562 (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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351B PHE* 4.3 13.2 - - + +
354B ILE* 4.7 8.1 - - + -
355B GLY* 3.8 20.2 - - - +
527B ILE* 5.2 6.5 - - + +
531B ALA* 4.5 10.9 - - + +
558B PRO 2.9 18.0 + - - +
559B MET* 4.0 5.2 - - - +
561B VAL* 1.3 78.4 - - + +
563B VAL* 1.3 57.6 + - - +
565B LEU* 3.4 11.2 + - - +
566B ALA* 3.0 30.3 + - - +
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Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 5.9 0.7 - - + -
527B ILE 5.3 0.2 - - - +
530B ALA* 4.0 13.0 - - + +
531B ALA* 3.9 27.5 - - + +
534B GLY* 5.3 4.4 - - - -
539B THR 4.1 1.8 - - - +
540B VAL* 4.0 22.9 - - + -
543B ALA* 3.7 25.6 - - + +
559B MET 2.9 21.9 + - - +
560B MET* 3.7 6.3 - - - +
562B ALA* 1.3 76.1 - - - +
564B ILE* 1.3 58.5 + - + +
566B ALA* 3.4 2.5 + - - +
567B ASN* 2.9 49.6 + - - +
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Residues in contact with ILE 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.6 31.9 - - + -
307A PHE* 3.9 32.1 - - + +
310A THR* 3.8 23.6 - - + -
540B VAL* 3.9 20.2 - - + -
560B MET 3.0 18.3 + - - +
561B VAL* 3.2 4.2 + - - +
563B VAL* 1.3 74.8 - - + +
565B LEU* 1.3 60.6 + - + +
567B ASN* 3.7 6.6 - - + +
568B MET* 3.0 40.1 + - + +
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Residues in contact with LEU 565 (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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351B PHE 5.2 0.4 - - - +
352B ALA* 4.5 24.2 - - + +
355B GLY* 4.4 2.7 - - - -
356B ILE* 3.7 28.3 - - + -
561B VAL* 2.9 36.7 + - + +
562B ALA* 3.6 10.5 - - - +
564B ILE* 1.3 76.1 - - - +
566B ALA* 1.3 62.9 + - - +
568B MET* 3.3 22.7 - - + +
569B VAL* 3.1 26.2 + - - +
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Residues in contact with ALA 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLY* 3.8 21.5 - - - +
358B CYS 5.0 0.2 - - - -
359B GLY* 4.0 10.0 - - - +
531B ALA* 4.0 13.5 - - + +
535B ALA* 3.7 23.3 - - + +
562B ALA 3.0 17.0 + - - +
563B VAL 3.9 3.1 - - - +
565B LEU* 1.3 77.1 - - - +
567B ASN* 1.3 57.1 + - - +
569B VAL* 3.5 3.9 + - - +
570B ALA* 2.9 31.0 + - - +
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Residues in contact with ASN 567 (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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534B GLY 2.8 29.5 - - - +
535B ALA* 3.8 1.4 - - - -
538B HIS* 4.2 6.4 - - - -
539B THR 2.5 29.9 + - - +
540B VAL* 3.4 13.4 - - + +
563B VAL* 2.9 36.7 + - - +
564B ILE* 3.7 7.2 - - + +
565B LEU 3.2 0.2 - - - -
566B ALA* 1.3 78.6 - - - +
568B MET* 1.3 58.3 + - - +
570B ALA* 3.8 3.8 - - - +
571B GLN* 2.8 32.8 + - - +
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Residues in contact with MET 568 (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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115A GLY* 6.6 0.2 - - - -
307A PHE* 4.4 19.1 - - + -
356B ILE* 6.0 0.2 - - + -
564B ILE* 3.0 36.8 + - + +
565B LEU* 3.3 29.6 - - + +
567B ASN* 1.3 74.9 - - - +
569B VAL* 1.3 62.3 + - + +
571B GLN* 3.8 11.9 - - - +
572B SER* 2.9 29.5 + - - -
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Residues in contact with VAL 569 (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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356B ILE* 3.9 36.8 - - + +
359B GLY 4.1 0.9 - - - -
360B LEU* 3.9 23.1 - - + +
565B LEU 3.1 18.5 + - - +
566B ALA* 3.8 5.6 - - - +
568B MET* 1.3 79.9 - - + +
570B ALA* 1.3 55.7 + - - +
572B SER* 3.2 8.2 + - - -
573B LEU* 3.0 47.8 + - + +
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Residues in contact with ALA 570 (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 GLY 4.8 9.2 - - - +
363B ALA* 5.0 7.9 - - + +
535B ALA* 3.3 31.2 - - + +
538B HIS* 3.6 11.9 - - + +
566B ALA 2.9 18.1 + - - +
567B ASN 3.8 2.0 - - - +
569B VAL* 1.3 75.2 - - - +
571B GLN* 1.3 63.4 + - - +
573B LEU* 4.4 3.4 - - - +
574B GLN* 2.8 33.2 + - + +
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Residues in contact with GLN 571 (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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303A TRP* 4.6 25.4 - - - -
538B HIS* 3.7 16.4 + - + +
567B ASN* 2.8 22.9 + - - +
568B MET* 3.9 11.1 - - - +
570B ALA* 1.3 72.9 - - - +
572B SER* 1.3 61.9 + - - +
573B LEU 3.6 0.3 + - - -
574B GLN 4.5 3.5 - - - +
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Residues in contact with SER 572 (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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568B MET 2.9 19.9 + - - -
569B VAL* 3.3 8.3 - - - -
571B GLN* 1.3 80.0 - - - +
573B LEU* 1.3 71.3 - - - +
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Residues in contact with LEU 573 (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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360B LEU* 4.6 18.2 - - + -
363B ALA* 4.3 16.4 - - + -
569B VAL* 3.0 37.8 + - + +
570B ALA 3.1 1.1 + - - +
571B GLN 4.9 0.4 - - - -
572B SER* 1.3 89.5 - - - +
574B GLN* 1.3 82.0 + - + +
575B PRO* 4.8 1.0 - - - +
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Residues in contact with GLN 574 (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 ALA* 3.7 41.5 - - + +
364B VAL* 5.6 0.2 - - - -
366B VAL* 5.1 4.0 - - + -
367B TYR* 4.2 15.1 - - + +
370B ARG* 2.6 33.2 + - - +
538B HIS* 3.4 5.9 + - - -
570B ALA* 2.8 17.9 + - - +
571B GLN 4.5 3.7 - - - +
573B LEU* 1.3 91.4 + - + +
575B PRO* 1.3 79.1 - - + +
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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