Contacts of the helix formed by residues 596 - 608 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561H LEU* 4.7 9.1 - - + +
589H LEU* 5.2 2.8 + - - +
590H LEU* 5.5 3.5 - - - +
593H HIS* 3.4 21.4 + - - +
594H GLY 2.8 28.1 + - - -
595H ARG* 1.3 77.0 - - - +
597H HIS* 1.3 64.0 + - - +
598H LYS* 3.3 6.0 + - + +
599H VAL* 3.5 28.9 + - + +
600H LEU* 3.3 20.2 - - - +
1662H PHE* 4.5 4.5 - - - -
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Residues in contact with HIS 597 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596H ASN* 1.3 72.3 - - - +
598H LYS* 1.3 73.0 + - - +
599H VAL 3.4 0.4 + - - -
600H LEU* 4.1 9.1 + - - -
601H ASP* 4.1 5.0 + - - +
1661H GLN* 3.5 25.6 - - + +
1662H PHE* 5.0 6.6 - - + +
1665H HIS* 2.8 47.3 + - + +
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Residues in contact with LYS 598 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558H SER* 6.0 2.2 - - - +
561H LEU* 3.7 23.6 - - + -
562H GLU* 6.5 0.4 - - - -
565H TYR* 4.8 4.4 - - + +
596H ASN* 3.2 3.0 - - + -
597H HIS* 1.3 102.5 - - - +
599H VAL* 1.3 63.0 + - - +
600H LEU 3.4 0.7 - - - -
601H ASP* 3.6 10.8 + - + +
602H VAL* 3.3 23.7 + - - +
1661H GLN* 4.1 10.4 - - - +
1665H HIS* 5.8 1.1 - - + -
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Residues in contact with VAL 599 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561H LEU* 3.7 33.0 - - + -
586H ILE* 4.2 15.0 - - + +
589H LEU* 4.6 11.4 - - + -
590H LEU* 3.8 33.7 - - + -
596H ASN* 3.5 27.3 + - + +
597H HIS 3.4 0.6 - - - -
598H LYS* 1.3 76.8 - - - +
600H LEU* 1.3 61.2 + - - +
602H VAL* 3.0 6.8 + - + +
603H LEU* 2.9 43.2 + - + +
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Residues in contact with LEU 600 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590H LEU* 5.0 10.8 - - + -
596H ASN 3.3 21.3 - - - +
597H HIS* 4.5 2.9 - - - +
598H LYS 3.4 0.6 - - - -
599H VAL* 1.3 79.6 - - + +
601H ASP* 1.3 57.8 + - - +
603H LEU* 3.3 9.7 + - - +
604H CYS* 2.9 28.8 + - - +
632H LEU* 4.7 8.3 - - + -
1662H PHE* 3.7 22.7 - - + -
1665H HIS* 3.5 25.8 - - + +
1666H THR* 3.5 42.0 - - - +
1669H LEU* 4.3 20.2 - - + +
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Residues in contact with ASP 601 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H TYR* 3.6 27.9 - - + +
597H HIS 4.1 7.5 + - - +
598H LYS* 3.6 14.6 + - + +
599H VAL 3.2 0.6 - - - -
600H LEU* 1.3 79.3 - - - +
602H VAL* 1.3 55.1 + - - +
604H CYS* 3.3 7.0 + - - +
605H SER* 2.9 30.1 + - - -
1665H HIS* 5.3 4.3 + - + -
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Residues in contact with VAL 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561H LEU* 4.0 18.4 - - + -
564H LEU* 4.3 17.5 - - + +
565H TYR* 3.6 31.6 - - + +
568H LEU* 4.0 23.1 - - + -
586H ILE* 5.0 9.6 - - + -
598H LYS 3.3 15.9 + - - +
599H VAL* 3.0 9.5 + - + +
601H ASP* 1.3 76.4 - - - +
603H LEU* 1.3 61.5 + - + +
605H SER* 3.0 8.8 + - - +
606H LEU* 2.9 30.9 + - + +
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Residues in contact with LEU 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583H ILE* 5.0 13.5 - - + -
586H ILE* 3.6 31.2 - - + -
587H ILE* 5.2 7.2 - - + -
590H LEU* 5.3 4.7 - - + -
599H VAL* 2.9 32.9 + - + +
600H LEU* 3.6 9.4 - - - +
602H VAL* 1.3 80.7 - - + +
604H CYS* 1.3 57.5 + - - +
606H LEU* 3.3 13.1 + - + +
607H CYS* 2.9 29.1 + - - +
621H ILE* 4.9 16.8 - - + -
625H LEU* 5.4 6.7 - - + -
1669H LEU* 3.8 27.4 - - + +
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Residues in contact with CYS 604 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600H LEU 2.9 16.5 + - - +
601H ASP* 3.7 7.9 - - - +
603H LEU* 1.3 76.7 - - - +
605H SER* 1.3 64.4 + - - +
607H CYS* 3.3 16.8 + - - +
608H VAL* 3.7 13.6 + - - +
1668H ARG* 4.8 19.7 - - + -
1669H LEU* 4.0 16.5 - - + +
1672H ALA* 4.1 21.5 - - + +
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Residues in contact with SER 605 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H TYR* 4.9 10.9 + - - -
568H LEU* 3.7 36.7 - - - +
569H ILE* 4.9 15.0 - - - -
575H LEU* 4.0 5.4 - - - +
601H ASP 2.9 14.5 + - - -
602H VAL* 3.0 14.1 + - - -
604H CYS* 1.3 77.4 - - - +
606H LEU* 1.3 61.0 + - - +
608H VAL* 3.0 23.0 - - - +
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Residues in contact with LEU 606 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568H LEU* 3.7 32.1 - - + -
575H LEU* 3.2 29.6 - - + +
578H ILE* 3.8 43.7 - - + -
582H HIS* 6.1 3.4 - - + -
583H ILE* 5.6 14.8 - - + +
586H ILE* 6.0 6.1 - - + -
602H VAL* 2.9 16.2 + - + +
603H LEU* 3.9 13.9 - - + +
605H SER* 1.3 79.4 + - - +
607H CYS* 1.3 64.4 + - - +
617H ASN* 4.0 13.9 - - + +
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Residues in contact with CYS 607 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603H LEU 2.9 16.9 + - - +
604H CYS* 3.5 10.8 - - - +
605H SER 3.2 0.8 - - - -
606H LEU* 1.3 80.2 - - - +
608H VAL* 1.3 61.8 + - + +
614H VAL* 3.5 22.3 + - - +
617H ASN* 5.2 3.6 - - - -
618H GLN* 3.4 36.9 + - - +
1669H LEU* 5.4 2.9 - - + -
1672H ALA* 3.4 29.4 - - + +
1673H VAL* 3.6 17.5 - - - -
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Residues in contact with VAL 608 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575H LEU* 4.4 1.2 - - - +
604H CYS* 3.7 14.1 + - - +
605H SER* 3.0 19.0 - - - +
607H CYS* 1.3 83.5 - - + +
609H CYS* 1.3 77.6 + - - +
611H GLY* 4.9 0.7 - - - +
612H VAL 3.3 12.6 - - - +
613H ALA* 4.5 5.2 - - + +
618H GLN* 5.3 2.5 - - - +
1672H ALA* 5.4 10.3 - - + +
1676H LEU* 4.1 31.9 - - + -
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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
------------------------------------------------------------
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