Contacts of the helix formed by residues 596 - 608 (chain B) in PDB entry 6X34
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 ASN 596 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B LEU* 4.7 9.3 - - + +
589B LEU* 5.2 2.8 + - - +
590B LEU* 5.5 2.9 - - - +
593B HIS* 3.4 22.0 + - - +
594B GLY 2.9 27.9 + - - -
595B ARG* 1.3 78.5 - - - +
597B HIS* 1.3 64.1 + - - +
598B LYS* 3.2 6.1 + - + +
599B VAL* 3.5 30.9 + - + +
600B LEU* 3.3 19.6 - - - +
1662B PHE* 4.5 4.4 - - - -
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Residues in contact with HIS 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B ASN* 1.3 71.4 - - - +
598B LYS* 1.3 74.3 + - - +
599B VAL 3.4 0.2 - - - -
600B LEU* 4.1 8.2 + - - -
601B ASP* 4.1 5.4 + - - +
1661B GLN* 3.5 25.6 - - + +
1662B PHE* 5.0 7.3 - - + +
1665B HIS* 2.8 48.1 + - + +
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Residues in contact with LYS 598 (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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558B SER* 6.0 2.2 - - - +
561B LEU* 3.7 23.8 - - + -
562B GLU* 6.5 0.4 - - - -
565B TYR* 4.8 3.6 - - + +
596B ASN* 3.2 3.2 - - + -
597B HIS* 1.3 104.4 - - - +
599B VAL* 1.3 62.5 + - - +
600B LEU 3.4 0.9 - - - -
601B ASP* 3.6 9.9 + - + +
602B VAL* 3.3 24.1 + - - +
1661B GLN* 4.1 10.6 - - - +
1665B HIS* 5.8 1.3 - - + -
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Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 3.7 33.9 - - + -
586B ILE* 4.2 15.0 - - + +
589B LEU* 4.6 11.9 - - + -
590B LEU* 3.8 33.0 - - + -
596B ASN* 3.5 28.0 + - + +
597B HIS 3.4 0.6 - - - -
598B LYS* 1.3 76.7 - - - +
600B LEU* 1.3 61.3 + - - +
602B VAL* 3.0 6.2 + - + +
603B LEU* 2.9 44.9 + - + +
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Residues in contact with LEU 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LEU* 5.0 10.1 - - + -
596B ASN 3.3 21.5 - - - +
597B HIS* 4.5 2.7 - - - +
598B LYS 3.4 0.4 - - - -
599B VAL* 1.3 79.9 - - + +
601B ASP* 1.3 58.0 + - - +
603B LEU* 3.3 10.1 + - + +
604B CYS* 2.9 28.8 + - - +
632B LEU* 4.7 8.5 - - + -
1662B PHE* 3.7 23.6 - - + -
1665B HIS* 3.5 25.4 - - + +
1666B THR* 3.5 42.2 - - - +
1669B LEU* 4.3 19.6 - - + +
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Residues in contact with ASP 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B TYR* 3.6 27.0 - - + +
597B HIS 4.1 6.3 + - - +
598B LYS* 3.6 15.7 + - + +
599B VAL 3.2 0.6 - - - -
600B LEU* 1.3 79.0 - - - +
602B VAL* 1.3 56.6 + - - +
604B CYS* 3.3 6.8 + - - +
605B SER* 2.9 29.6 + - - -
1665B HIS* 5.3 4.8 + - + -
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Residues in contact with VAL 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 4.0 17.9 - - + -
564B LEU* 4.3 17.9 - - + +
565B TYR* 3.6 30.7 - - + +
568B LEU* 4.0 22.7 - - + -
586B ILE* 5.0 9.6 - - + -
598B LYS 3.3 16.4 - - - +
599B VAL* 3.0 9.9 + - + +
601B ASP* 1.3 77.0 - - - +
603B LEU* 1.3 60.0 + - + +
605B SER* 3.0 8.0 + - - +
606B LEU* 2.9 30.8 + - + +
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Residues in contact with LEU 603 (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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583B ILE* 5.0 12.3 - - + -
586B ILE* 3.6 31.4 - - + -
587B ILE* 5.2 7.0 - - + -
590B LEU* 5.3 5.2 - - + -
599B VAL* 2.9 32.8 + - + +
600B LEU* 3.3 9.8 + - - +
602B VAL* 1.3 80.6 - - + +
604B CYS* 1.3 57.1 + - - +
606B LEU* 3.3 13.8 + - + +
607B CYS* 2.9 29.3 + - - +
621B ILE* 4.9 17.3 - - + -
625B LEU* 5.4 7.6 - - + -
1669B LEU* 3.8 26.8 - - + +
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Residues in contact with CYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LEU 2.9 17.8 + - - +
601B ASP* 3.3 8.0 + - - +
603B LEU* 1.3 75.4 - - - +
605B SER* 1.3 62.8 + - - +
607B CYS* 3.3 16.9 + - - +
608B VAL* 3.7 13.8 + - - +
1668B ARG* 4.8 19.7 - - + -
1669B LEU* 4.0 16.1 - - + +
1672B ALA* 4.1 20.9 - - + -
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Residues in contact with SER 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B TYR* 4.9 11.1 + - - -
568B LEU* 3.7 35.9 - - - +
569B ILE* 4.9 13.7 - - - -
575B LEU* 4.0 5.2 - - - +
601B ASP 2.9 15.6 + - - -
602B VAL* 3.0 13.9 + - - -
604B CYS* 1.3 78.7 - - - +
606B LEU* 1.3 61.0 + - - +
608B VAL* 3.0 23.5 - - - +
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 3.7 31.6 - - + -
575B LEU* 3.2 29.9 - - + +
578B ILE* 3.8 43.1 - - + -
582B HIS* 6.1 3.6 - - + -
583B ILE* 5.6 14.4 - - + +
586B ILE* 6.0 5.8 - - + -
602B VAL* 2.9 16.5 + - + +
603B LEU* 3.6 14.8 - - + +
605B SER* 1.3 78.9 + - - +
607B CYS* 1.3 65.4 + - - +
617B ASN* 4.0 13.4 - - + +
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Residues in contact with CYS 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU 2.9 16.1 + - - +
604B CYS* 3.5 11.2 - - - +
605B SER 3.2 1.0 - - - -
606B LEU* 1.3 80.3 - - - +
608B VAL* 1.3 60.5 + - + +
614B VAL* 3.5 22.5 + - - +
617B ASN* 5.2 3.8 - - - -
618B GLN* 3.4 36.8 + - - +
1669B LEU* 5.4 4.3 - - + -
1672B ALA* 3.4 29.4 - - + +
1673B VAL* 3.6 17.0 - - - -
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Residues in contact with VAL 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 4.4 1.5 - - - +
604B CYS* 3.7 14.5 + - - +
605B SER* 3.0 19.6 - - - +
607B CYS* 1.3 82.6 - - + +
609B CYS* 1.3 77.2 + - - +
611B GLY* 4.9 0.7 - - - +
612B VAL 3.3 12.8 - - - +
613B ALA* 4.5 4.7 - - + +
618B GLN* 5.3 2.5 - - - +
1672B ALA* 5.4 11.0 - - + +
1676B LEU* 4.1 31.6 - - + -
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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