Contacts of the helix formed by residues 610 - 621 (chain X) 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 PRO 610 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608X THR 3.9 1.6 - - - -
609X MET* 1.3 77.9 - - - +
611X PRO* 1.3 67.2 - - - +
612X ALA 3.3 2.9 - - - -
613X VAL* 3.0 15.5 + - - +
614X GLU* 3.1 9.5 + - - -
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Residues in contact with PRO 611 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610X PRO* 1.3 71.4 - - - +
612X ALA* 1.3 56.2 + - - +
614X GLU* 3.1 4.6 + - - +
615X ARG* 2.9 25.1 + - - -
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Residues in contact with ALA 612 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610X PRO 3.3 1.0 - - - -
611X PRO* 1.3 75.4 - - - +
613X VAL* 1.3 61.4 + - - +
615X ARG* 3.3 2.7 + - - +
616X LEU* 3.1 18.4 + - - -
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Residues in contact with VAL 613 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551X ALA 5.8 7.0 - - - -
552X ASP* 6.1 2.7 - - - +
609X MET* 5.8 2.7 - - - +
610X PRO 3.0 11.0 + - - -
612X ALA* 1.3 76.3 - - - +
614X GLU* 1.3 58.6 + - - +
616X LEU* 3.2 2.9 + - - +
617X ALA* 3.0 23.0 + - - -
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Residues in contact with GLU 614 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609X MET* 5.6 0.4 - - - +
610X PRO 3.1 8.7 + - - -
611X PRO* 3.1 8.5 + - - -
613X VAL* 1.3 74.3 - - - +
615X ARG* 1.3 58.6 + - - +
617X ALA* 3.3 2.6 + - - +
618X ARG* 2.9 25.3 + - - -
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Residues in contact with ARG 615 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611X PRO 2.9 13.6 + - - -
612X ALA* 3.3 4.5 + - - +
613X VAL 3.3 0.4 - - - -
614X GLU* 1.3 73.9 - - - +
616X LEU* 1.3 63.9 + - - +
618X ARG* 3.3 2.6 + - - +
619X SER* 3.2 18.5 + - - -
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Residues in contact with LEU 616 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612X ALA 3.1 13.8 + - - -
613X VAL* 3.2 4.6 + - - +
615X ARG* 1.3 75.1 - - - +
617X ALA* 1.3 53.4 + - - +
619X SER* 3.2 1.9 + - - -
620X TYR* 2.7 34.5 + - - -
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Residues in contact with ALA 617 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613X VAL 3.0 14.2 + - - -
614X GLU* 3.3 3.8 + - - +
615X ARG 3.2 0.2 - - - -
616X LEU* 1.3 77.3 - - - +
618X ARG* 1.3 55.6 + - - +
620X TYR* 4.6 0.4 - - - +
621X LEU* 2.9 33.7 + - - +
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Residues in contact with ARG 618 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614X GLU 2.9 14.8 + - - -
615X ARG* 3.3 4.0 + - - +
617X ALA* 1.3 75.3 - - - +
619X SER* 1.3 61.2 + - - +
621X LEU 3.9 8.9 - - - +
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Residues in contact with SER 619 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615X ARG 3.2 12.1 + - - -
616X LEU* 3.6 1.8 - - - +
618X ARG* 1.3 78.6 - - - +
620X TYR* 1.3 64.8 + - - +
621X LEU 3.5 1.9 + - - +
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Residues in contact with TYR 620 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602X THR* 5.0 9.2 + - - -
616X LEU 2.7 19.0 + - - -
617X ALA* 5.2 0.2 - - - +
619X SER* 1.3 73.5 - - - +
621X LEU* 1.3 57.6 + - - +
622X ARG 4.3 0.2 + - - -
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Residues in contact with LEU 621 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602X THR* 5.5 9.9 - - - +
617X ALA* 2.9 20.6 + - - +
618X ARG* 3.9 10.2 - - - +
619X SER 4.5 1.1 - - - +
620X TYR* 1.3 78.9 - - - +
622X ARG* 1.3 60.4 + - - +
623X ARG 4.2 0.7 + - - -
624X PRO* 5.2 3.1 - - - -
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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