Contacts of the helix formed by residues 615 - 626 (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 CYS 615 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613H ALA 4.7 0.4 - - - -
614H VAL* 1.3 78.5 - - - +
616H SER* 1.3 61.1 + - - +
617H ASN 3.5 0.7 - - - -
618H GLN* 4.0 4.3 - - - +
619H ASP* 3.1 35.2 + - - +
1678H ASN* 4.2 18.1 + - - +
2169H VAL* 4.5 21.1 - - - -
2170H GLN* 5.1 1.7 + - - -
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Residues in contact with SER 616 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H ILE* 5.9 2.6 - - - +
614H VAL* 4.7 6.6 - - - +
615H CYS* 1.3 76.2 + - - +
617H ASN* 1.3 62.1 + - - +
619H ASP* 3.3 5.3 + - - +
620H LEU* 2.9 38.7 + - - +
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Residues in contact with ASN 617 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575H LEU* 5.4 0.2 - - + -
578H ILE* 4.0 26.9 - - + +
583H ILE* 4.4 3.4 - - + +
606H LEU* 4.0 16.6 - - + +
607H CYS* 5.0 2.9 - - - +
614H VAL* 3.9 20.7 - - + +
615H CYS 3.5 0.2 - - - -
616H SER* 1.3 80.9 + - - +
618H GLN* 1.3 58.9 + - - +
620H LEU* 3.3 10.4 + - - +
621H ILE* 2.9 30.4 + - - +
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Residues in contact with GLN 618 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607H CYS* 3.4 40.3 + - - +
608H VAL* 5.3 2.4 - - - +
613H ALA* 4.6 13.3 - - - +
614H VAL* 3.4 21.2 + - + +
615H CYS 3.7 4.1 + - - +
616H SER 3.3 0.4 - - - -
617H ASN* 1.3 76.0 - - - +
619H ASP* 1.3 59.1 + - - +
621H ILE* 3.3 6.3 + - - +
622H THR* 2.7 34.1 + - - +
1672H ALA 4.5 3.0 + - - -
1673H VAL* 2.9 31.2 + - + +
1675H ALA 4.8 6.1 + - - -
1678H ASN* 2.4 37.2 + - - +
1681H VAL* 4.3 3.8 - - + +
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Residues in contact with ASP 619 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G PRO* 5.6 9.9 - - - +
615H CYS* 3.1 22.6 + - - +
616H SER* 3.8 5.2 - - - +
618H GLN* 1.3 78.7 - - - +
620H LEU* 1.3 59.1 + - + +
622H THR* 3.3 8.4 + - - -
623H GLU* 2.9 30.9 + - - +
1678H ASN* 5.8 0.7 + - - +
1680H ARG* 3.9 36.3 + - - +
1681H VAL* 5.6 4.7 - - - +
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Residues in contact with LEU 620 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H ILE* 6.3 2.5 - - + -
579H GLN* 4.2 4.9 - - - +
580H GLU* 3.8 40.8 - - + +
583H ILE* 3.7 20.0 - - + -
616H SER* 2.9 27.2 + - - +
617H ASN* 3.7 7.6 - - - +
618H GLN 3.3 0.2 - - - -
619H ASP* 1.3 77.7 - - + +
621H ILE* 1.3 55.5 + - - +
623H GLU* 3.3 5.3 + - + -
624H ASN* 2.9 44.9 + - - +
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Residues in contact with ILE 621 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583H ILE* 3.5 15.8 - - + +
587H ILE* 6.4 0.7 - - - -
603H LEU* 4.9 13.7 - - + -
617H ASN 2.9 18.6 + - - +
618H GLN* 3.7 7.0 - - - +
620H LEU* 1.3 75.5 - - - +
622H THR* 1.3 56.7 + - - +
624H ASN* 5.1 0.7 - - - -
625H LEU* 2.9 45.2 + - + +
1669H LEU* 6.5 0.9 - - + -
1673H VAL* 5.1 9.0 - - + -
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Residues in contact with THR 622 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PRO* 3.4 29.6 - - + +
89G GLY* 3.4 5.2 - - - -
618H GLN 2.7 22.5 + - - -
619H ASP* 3.7 9.5 + - - -
621H ILE* 1.3 77.5 - - - +
623H GLU* 1.3 56.7 + - - +
626H LEU* 3.6 28.1 - - + +
627H PRO* 3.2 21.0 - - - +
1673H VAL* 4.4 5.0 - - - +
1681H VAL* 3.2 26.0 - - + +
1684H ALA* 4.1 8.3 - - + -
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Residues in contact with GLU 623 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PRO* 5.4 7.6 - - + +
89G GLY 4.9 4.0 - - - +
619H ASP 2.9 17.3 + - - +
620H LEU* 3.9 7.0 - - + +
622H THR* 1.3 79.1 - - - +
624H ASN* 1.3 67.4 + - - +
625H LEU 3.6 0.4 - - - -
627H PRO* 3.3 23.2 - - - +
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Residues in contact with ASN 624 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580H GLU* 5.8 1.0 - - - +
583H ILE* 4.6 12.5 - - + +
584H LYS* 6.2 3.4 - - - -
587H ILE* 4.1 32.7 - - + +
620H LEU* 2.9 38.8 + - - +
621H ILE* 3.7 0.7 - - - +
623H GLU* 1.3 84.1 + - - +
625H LEU* 1.3 59.4 + - - +
627H PRO* 4.7 1.1 - - - -
628H GLY* 5.5 3.0 + - - -
631H LEU* 5.4 2.6 - - - +
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Residues in contact with LEU 625 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587H ILE* 5.0 15.9 - - + -
590H LEU* 6.3 3.4 - - + -
603H LEU* 5.4 7.2 - - + -
621H ILE* 2.9 26.9 + - + +
623H GLU 3.6 0.4 - - - -
624H ASN* 1.3 80.8 - - - +
626H LEU* 1.3 84.5 + - + +
627H PRO 3.7 0.2 - - - -
628H GLY* 3.8 8.9 + - - -
629H ARG 4.1 5.5 + - - -
631H LEU* 5.7 7.5 - - + +
632H LEU* 4.0 30.1 - - + +
1669H LEU* 4.2 23.6 - - + -
1670H TYR* 4.0 18.6 - - + +
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Residues in contact with LEU 626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G GLY* 3.2 18.6 - - - +
622H THR* 3.6 33.5 + - + +
625H LEU* 1.3 85.4 - - + +
627H PRO* 1.3 71.1 - - + +
628H GLY 3.1 3.4 + - - -
629H ARG* 3.3 24.8 + - - +
1670H TYR* 3.7 32.8 - - + +
1681H VAL* 5.6 2.5 - - + -
1684H ALA* 4.1 12.3 - - + +
1685H LEU* 4.8 4.3 - - + +
1688H HIS* 3.6 35.8 - - + +
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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
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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