Contacts of the helix formed by residues 599 - 614 (chain C) in PDB entry 6AH0
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 GLU 599 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594C PRO* 6.3 1.1 - - - -
596C ASN 3.1 12.8 + - - -
598C SER* 1.3 75.6 - - - +
600C LEU* 1.3 64.0 + - - +
601C PRO 3.4 2.5 - - - -
602C LYS* 2.9 17.1 + - - +
603C MET* 3.3 7.8 + - - -
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Residues in contact with LEU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C PRO* 6.2 4.5 - - - -
596C ASN 4.0 1.6 + - - -
597C PRO* 3.1 14.8 + - - -
598C SER 3.3 1.6 - - - -
599C GLU* 1.3 77.4 - - - +
601C PRO* 1.4 56.5 - - - +
603C MET* 3.1 5.1 + - - +
604C LEU* 3.0 24.1 + - - -
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Residues in contact with PRO 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C SER 5.0 1.6 - - - -
599C GLU 3.2 1.0 - - - -
600C LEU* 1.4 70.7 - - - +
602C LYS* 1.3 60.1 + - - +
603C MET 3.3 0.2 - - - -
604C LEU* 3.7 2.9 - - - +
605C ASP* 3.0 23.4 + - - -
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Residues in contact with LYS 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C GLU 2.9 10.3 + - - -
601C PRO* 1.3 75.8 - - - +
603C MET* 1.3 64.3 + - - +
605C ASP* 3.2 3.3 + - - +
606C GLY* 3.0 18.2 + - - -
648C TYR 5.5 0.3 - - - +
649C SER* 5.1 8.7 - - - -
305W LEU* 5.3 14.3 - - - +
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Residues in contact with MET 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C GLU 3.3 6.4 + - - -
600C LEU* 3.1 7.4 + - - +
602C LYS* 1.3 77.3 - - - +
604C LEU* 1.3 55.7 + - - +
606C GLY* 3.0 4.7 + - - +
607C LEU* 2.9 24.6 + - - -
649C SER* 6.1 2.2 - - - +
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Residues in contact with LEU 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C LEU 3.0 12.8 + - - -
601C PRO* 3.5 4.7 + - - -
602C LYS 3.2 0.2 - - - -
603C MET* 1.3 75.9 - - - +
605C ASP* 1.3 60.9 + - - +
607C LEU* 3.2 4.2 + - - +
608C ARG* 3.0 18.9 + - - -
128W LEU 5.0 11.9 - - - +
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Residues in contact with ASP 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C PRO 3.0 14.7 + - - -
602C LYS* 3.2 4.7 + - - +
604C LEU* 1.3 75.6 - - - +
606C GLY* 1.3 62.6 + - - +
608C ARG* 3.1 11.2 + - - +
609C LYS* 3.2 10.6 + - - -
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Residues in contact with GLY 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C LYS 3.0 12.7 + - - -
603C MET* 3.0 5.8 + - - -
605C ASP* 1.3 76.8 - - - +
607C LEU* 1.3 60.8 + - - +
609C LYS* 3.2 5.0 + - - -
610C VAL* 3.1 18.0 + - - -
644C LEU* 5.7 5.8 - - - -
648C TYR* 4.6 25.7 + - - -
649C SER* 4.8 3.1 - - - -
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Residues in contact with LEU 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C MET 2.9 12.1 + - - -
604C LEU* 3.2 5.1 + - - +
606C GLY* 1.3 74.1 - - - +
608C ARG* 1.3 61.5 + - - +
610C VAL* 3.2 2.8 + - - +
611C ASN* 3.1 19.1 + - - -
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Residues in contact with ARG 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C LEU 3.0 12.3 + - - -
605C ASP* 3.1 5.7 + - - +
607C LEU* 1.3 74.3 - - - +
609C LYS* 1.3 63.3 + - - +
611C ASN* 3.1 11.7 + - - +
612C LYS* 3.2 9.5 + - - -
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Residues in contact with LYS 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C VAL* 5.5 8.1 - - - +
605C ASP 3.2 8.8 + - - -
606C GLY 3.2 8.1 + - - -
608C ARG* 1.3 76.7 - - - +
610C VAL* 1.3 56.5 + - - +
612C LYS* 3.1 3.9 + - - +
613C SER* 2.9 24.1 + - - -
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Residues in contact with VAL 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C GLY 3.1 13.1 + - - -
607C LEU* 3.2 3.7 + - - +
609C LYS* 1.3 76.6 - - - +
611C ASN* 1.3 57.3 + - - +
613C SER* 4.2 2.9 - - - +
614C TYR* 2.9 28.9 + - - -
617C LEU* 5.9 1.6 - - - -
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Residues in contact with ASN 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C LYS* 4.7 9.4 + - - -
607C LEU 3.1 14.0 + - - -
608C ARG* 3.1 5.8 + - - +
610C VAL* 1.3 74.8 - - - +
612C LYS* 1.3 55.8 + - - +
614C TYR 3.0 19.1 - - - +
615C PRO 5.0 1.0 - - - +
617C LEU 4.6 13.7 - - - +
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Residues in contact with LYS 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C MET* 4.4 17.0 + - - -
560C VAL* 5.7 1.8 - - - +
561C LYS* 4.6 18.9 - - - +
608C ARG 3.2 7.4 + - - -
609C LYS* 3.1 7.4 + - - +
610C VAL 3.1 0.6 - - - -
611C ASN* 1.3 77.4 - - - +
613C SER* 1.3 63.1 + - - +
614C TYR 3.5 3.5 + - - +
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Residues in contact with SER 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C MET 4.2 17.6 + - - +
609C LYS 2.9 14.1 + - - -
610C VAL* 3.2 4.2 + - - +
612C LYS* 1.3 78.7 - - - +
614C TYR* 1.3 56.2 + - - +
615C PRO 4.2 0.5 - - - -
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Residues in contact with TYR 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C LYS* 5.7 1.7 - - - -
610C VAL 2.9 12.8 + - - +
611C ASN* 3.0 21.3 - - - +
612C LYS 4.0 3.1 - - - +
613C SER* 1.3 77.1 - - - +
615C PRO* 1.3 67.0 - - - +
616C SER 3.9 0.2 - - - -
617C LEU* 4.4 8.5 + - - +
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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