Contacts of the helix formed by residues 615 - 624 (chain C) in PDB entry 2A2N
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 GLY 615 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C ASP 3.5 17.7 - - - -
503C ILE* 4.5 1.7 - - - +
612C VAL* 4.2 3.8 - - - -
614C LYS* 1.3 81.3 - - - +
616C MET* 1.3 61.4 + - - +
617C GLU* 3.1 18.4 + - - -
618C VAL* 2.9 21.4 + - - +
619C VAL* 3.0 15.8 + - - +
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Residues in contact with MET 616 (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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576C TYR* 3.7 42.7 - - + +
612C VAL* 3.3 39.0 - - + +
613C THR* 4.2 14.1 - - - +
614C LYS* 4.9 1.8 - - - +
615C GLY* 1.3 79.1 - - - +
617C GLU* 1.3 58.9 + - - +
619C VAL* 3.3 4.6 + - - +
620C GLN* 3.0 32.6 + - - +
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Residues in contact with GLU 617 (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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615C GLY* 3.1 21.0 + - - -
616C MET* 1.3 75.8 + - - +
618C VAL* 1.3 71.0 + - - +
620C GLN* 3.4 9.1 + - - +
621C ARG* 2.9 55.0 + - - +
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Residues in contact with VAL 618 (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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500C MET* 3.4 33.2 - - + +
501C GLY* 3.9 18.6 - - - +
502C ASP 3.9 16.6 - - - +
503C ILE* 4.0 8.3 - - + -
615C GLY* 2.9 10.5 + - - +
617C GLU* 1.3 92.7 - - + +
619C VAL* 1.3 66.7 + - - +
621C ARG* 3.2 12.8 + - - +
622C ILE* 2.9 43.2 + - + +
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Residues in contact with VAL 619 (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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503C ILE* 3.9 33.0 - - + -
542C ILE* 3.9 22.4 - - + +
576C TYR* 3.9 16.2 - - + -
594C ILE* 4.0 13.5 - - + +
596C VAL* 3.6 22.7 - - + -
612C VAL* 4.2 12.6 - - + -
615C GLY 3.0 13.5 + - - +
616C MET 3.3 6.3 + - - +
618C VAL* 1.3 76.8 - - - +
620C GLN* 1.3 62.5 + - - +
622C ILE* 3.2 3.4 + - - +
623C SER* 3.0 21.1 + - - -
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Residues in contact with GLN 620 (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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576C TYR* 2.8 30.5 + - + +
596C VAL* 3.6 26.5 - - - +
616C MET 3.0 13.0 + - - +
617C GLU* 3.6 11.4 - - - +
618C VAL 3.3 0.2 - - - -
619C VAL* 1.3 74.4 - - - +
621C ARG* 1.3 64.4 + - - +
623C SER* 2.7 30.8 + - - -
624C ASN* 3.0 24.4 + - - +
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Residues in contact with ARG 621 (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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500C MET* 2.9 44.9 + - + -
617C GLU* 2.9 50.8 + - - +
618C VAL* 3.2 11.1 + - - +
620C GLN* 1.3 71.7 - - - +
622C ILE* 1.3 64.8 + - - +
624C ASN* 3.1 16.6 + - - +
625C VAL* 3.5 12.3 + - - +
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Residues in contact with ILE 622 (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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498C THR* 3.9 31.6 - - + +
500C MET* 3.8 24.5 - - + -
503C ILE* 4.2 9.9 - - + -
533C PHE* 4.3 12.1 - - + -
536C ILE* 3.4 22.9 - - + +
542C ILE* 3.7 21.8 - - + -
618C VAL* 2.9 28.4 + - + +
619C VAL 3.6 4.5 - - - +
621C ARG* 1.3 75.4 - - - +
623C SER* 1.3 63.1 + - - +
624C ASN 3.1 1.2 + - - -
625C VAL* 3.3 23.1 + - - +
638C VAL* 4.1 14.6 - - + -
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Residues in contact with SER 623 (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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536C ILE* 3.5 12.0 - - - +
537C ILE 5.0 2.0 - - - -
538C LYS* 3.4 28.7 + - - +
539C GLY 4.9 1.2 + - - -
541C MET 5.2 0.2 - - - -
542C ILE* 3.6 22.0 - - - +
596C VAL* 3.8 24.0 - - - +
619C VAL 3.0 12.0 + - - -
620C GLN* 2.7 30.7 + - - -
622C ILE* 1.3 76.4 - - - +
624C ASN* 1.3 62.6 + - - +
625C VAL 3.5 2.1 - - - +
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Residues in contact with ASN 624 (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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538C LYS* 2.9 48.6 + - - +
539C GLY 5.2 0.6 - - - +
620C GLN* 3.0 27.3 + - - +
621C ARG* 3.1 11.1 + - - +
622C ILE 3.1 0.8 - - - -
623C SER* 1.3 83.8 + - - +
625C VAL* 1.3 66.2 + - - +
626C LYS* 3.8 10.4 + - - +
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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