Contacts of the helix formed by residues 665 - 682 (chain B) in PDB entry 4YZC
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 PRO 665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652B TYR* 3.9 18.1 - - + +
664B GLU* 1.3 92.6 - - + +
666B ILE* 1.3 68.9 + - + +
668B LEU* 3.2 10.3 + - + +
669B LEU* 3.1 27.7 + - + +
767B VAL* 3.5 28.8 - - + +
768B ILE* 6.1 2.0 - - + -
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Residues in contact with ILE 666 (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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664B GLU* 3.3 10.3 - - + +
665B PRO* 1.3 84.0 - - + +
667B THR* 1.3 59.0 + - - +
669B LEU* 3.2 8.0 + - + +
670B GLN* 2.9 26.8 + - - +
768B ILE* 6.1 1.6 - - + -
831B PHE* 3.9 39.0 - - + +
832B PHE* 3.5 30.1 - - + -
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Residues in contact with THR 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B GLU* 3.1 29.0 + - - +
666B ILE* 1.3 79.4 - - - +
668B LEU* 1.3 57.8 + - - +
670B GLN* 3.3 17.5 + - - +
671B GLN* 2.8 56.8 + - + +
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 4.1 17.3 - - + -
652B TYR* 3.6 45.1 - - + +
664B GLU 3.2 16.4 + - - +
665B PRO* 3.2 9.5 + - + +
667B THR* 1.3 77.7 - - - +
669B LEU* 1.3 55.9 + - + +
671B GLN* 3.3 8.2 + - - +
672B THR* 2.7 38.7 + - - +
696B ILE* 4.1 15.9 - - + -
705B ILE* 4.9 6.1 - - + +
706B LYS* 4.3 4.9 - - - +
707B ALA* 3.6 33.6 - - + +
767B VAL* 5.8 0.7 - - + -
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Residues in contact with LEU 669 (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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649B LEU* 5.0 3.8 - - + -
665B PRO* 3.1 15.7 + - + +
666B ILE* 3.6 8.1 - - + +
668B LEU* 1.3 75.7 - - + +
670B GLN* 1.3 57.7 + - - +
672B THR* 3.3 7.5 + - - +
673B THR* 2.7 38.4 + - - -
763B VAL* 4.2 9.6 - - + +
764B PHE* 3.8 53.5 - - + +
767B VAL* 3.7 34.5 - - + -
768B ILE* 4.4 3.4 - - + -
831B PHE* 4.1 25.4 - - + -
832B PHE* 4.2 3.4 - - + -
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Residues in contact with GLN 670 (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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666B ILE 2.9 16.9 + - - +
667B THR* 3.7 19.5 + - - +
669B LEU* 1.3 75.8 - - - +
671B GLN* 1.3 59.4 + - + +
673B THR* 3.3 3.5 + - - -
674B SER* 2.9 30.1 + - - -
827B LEU* 3.8 19.2 + - + +
832B PHE* 3.5 42.5 + - + +
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Residues in contact with GLN 671 (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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624B ASN* 3.3 38.3 - - - +
667B THR* 2.8 43.1 + - + +
668B LEU* 3.6 12.9 - - - +
670B GLN* 1.3 73.0 - - + +
672B THR* 1.3 65.4 + - - +
674B SER* 3.3 1.9 + - - -
675B GLY 3.0 18.9 + - - -
705B ILE 4.2 5.7 + - - +
706B LYS* 3.3 24.2 - - - +
707B ALA* 2.9 25.6 + - + +
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Residues in contact with THR 672 (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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624B ASN* 5.3 0.4 - - - -
649B LEU* 5.2 2.8 - - - +
668B LEU 2.7 22.5 + - - -
669B LEU* 3.7 10.5 - - - +
671B GLN* 1.3 75.7 - - - +
673B THR* 1.3 58.3 + - - +
675B GLY 3.5 0.3 + - - -
676B LEU* 2.9 28.2 + - + +
689B LEU* 4.9 10.1 - - + -
694B ILE* 3.6 38.3 - - + +
707B ALA* 3.6 17.3 - - - +
708B MET 6.2 0.2 - - - -
709B ILE* 3.5 18.9 - - + +
760B ALA* 6.2 2.7 - - + -
763B VAL* 5.6 2.2 - - + -
764B PHE* 5.6 4.3 - - + -
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Residues in contact with THR 673 (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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669B LEU 2.7 21.6 + - - -
670B GLN* 3.7 4.7 - - - -
672B THR* 1.3 76.5 - - - +
674B SER* 1.3 54.8 + - - +
676B LEU* 3.2 9.2 + - + +
677B ALA* 2.7 34.1 + - - +
757B ILE* 6.1 0.7 - - + -
760B ALA* 5.7 1.7 - - - +
764B PHE* 3.1 23.8 - - - -
823B ALA* 3.6 31.6 - - + +
826B VAL* 4.0 16.4 - - + -
827B LEU* 3.8 13.5 - - + -
832B PHE* 4.5 0.8 - - - -
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Residues in contact with SER 674 (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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622B HIS* 3.0 28.4 + - - -
624B ASN* 3.9 5.3 + - - -
670B GLN* 2.9 19.1 + - - -
671B GLN* 3.8 5.2 - - - -
673B THR* 1.3 76.1 - - - +
675B GLY* 1.3 58.0 + - - +
677B ALA* 3.4 2.8 + - - +
678B HIS* 2.9 22.9 + - - +
827B LEU* 3.9 20.6 - - - +
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Residues in contact with GLY 675 (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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622B HIS* 3.5 20.2 - - - -
624B ASN* 4.1 4.9 - - - -
625B VAL* 4.1 8.0 - - - +
671B GLN 3.0 14.4 + - - -
672B THR 3.9 2.2 - - - -
674B SER* 1.3 74.8 - - - +
676B LEU* 1.3 62.4 + - - +
678B HIS* 3.3 4.7 + - - +
679B LEU* 3.1 25.3 + - - +
709B ILE* 3.5 12.3 - - - -
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Residues in contact with LEU 676 (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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672B THR* 2.9 18.9 + - + +
673B THR* 3.2 10.3 + - + +
675B GLY* 1.3 74.6 - - - +
677B ALA* 1.3 59.8 + - - +
679B LEU* 3.1 9.8 + - + +
680B HIS* 2.9 55.3 + - + +
686B HIS* 4.4 12.8 - - + -
689B LEU* 4.1 16.6 - - + -
709B ILE* 3.3 12.9 - - + +
756B ASP* 3.8 41.5 - - + +
757B ILE* 4.4 10.8 - - + -
760B ALA* 4.4 7.2 - - + -
823B ALA* 4.8 3.4 - - + -
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Residues in contact with ALA 677 (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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673B THR 2.7 21.5 + - - +
674B SER 3.7 4.9 - - - +
675B GLY 3.3 0.2 - - - -
676B LEU* 1.3 73.0 - - - +
678B HIS* 1.3 57.5 + - - +
680B HIS* 3.4 4.9 + - - +
681B SER* 3.0 29.8 + - - -
823B ALA* 3.6 21.9 - - + +
824B LYS* 4.5 17.9 - - + -
827B LEU* 4.1 18.2 - - + -
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Residues in contact with HIS 678 (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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702A HIS* 5.0 9.5 + + - -
618B GLU 4.7 1.4 + - - -
619B SER* 3.3 40.4 + - - -
621B GLU* 4.9 6.4 + - + +
622B HIS* 3.6 38.9 + + + +
625B VAL* 4.4 2.5 - - + -
674B SER 2.9 13.3 + - - +
675B GLY 3.4 9.0 - - - +
676B LEU 3.2 0.2 - - - -
677B ALA* 1.3 77.2 - - - +
679B LEU* 1.3 61.8 + - - +
681B SER* 2.6 23.8 + - - -
682B LEU* 3.3 30.6 - - + +
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Residues in contact with LEU 679 (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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619B SER* 3.3 35.9 - - - +
625B VAL* 4.2 7.9 - - + -
675B GLY 3.1 18.8 + - - +
676B LEU* 3.1 13.7 + - + +
678B HIS* 1.3 76.8 - - - +
680B HIS* 1.3 65.3 + - + +
682B LEU* 3.0 16.6 + - - +
684B ILE* 3.0 41.4 + - + +
686B HIS* 3.8 37.2 - - + -
709B ILE* 4.3 9.4 - - + -
712B PHE* 3.8 17.0 - - + -
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Residues in contact with HIS 680 (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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676B LEU* 2.9 42.6 + - + +
677B ALA* 3.9 5.8 - - - +
679B LEU* 1.3 76.7 - - + +
681B SER* 1.3 57.2 + - - +
683B ASN* 3.0 21.0 + - - +
684B ILE 3.3 18.6 - - - -
753B TYR* 3.5 55.1 + + + +
756B ASP* 3.1 26.2 + - + -
757B ILE* 4.4 10.1 - - + -
822B SER* 6.0 1.2 - - - -
823B ALA* 4.2 14.1 + - + +
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Residues in contact with SER 681 (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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702A HIS* 3.2 39.5 + - - -
677B ALA 3.0 13.3 + - - -
678B HIS* 2.6 28.2 + - - -
680B HIS* 1.3 77.3 - - - +
682B LEU* 1.3 56.3 + - - +
683B ASN* 3.3 8.4 + - - +
824B LYS* 5.0 15.9 - - - -
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Residues in contact with LEU 682 (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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701A ALA* 3.5 30.3 - - + -
702A HIS* 3.6 22.2 - - + +
618B GLU* 4.0 20.4 - - + +
619B SER* 3.6 35.7 - - - +
678B HIS* 3.3 28.9 - - + +
679B LEU 3.0 9.1 + - - +
681B SER* 1.3 74.5 - - - +
683B ASN* 1.3 72.1 + - - +
684B ILE* 4.0 11.0 - - + -
717B LYS* 3.3 18.7 - - - +
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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