Contacts of the helix formed by residues 668 - 677 (chain A) in PDB entry 2HHT
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 ASP 668 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A ALA 3.6 4.7 + - - +
666A ALA* 3.1 3.3 - - + -
667A GLU* 1.3 76.3 - - - +
669A ASP* 1.3 58.4 + - - +
670A ASN* 3.0 13.0 + - - +
671A LEU* 2.9 35.7 + - + -
672A MET* 2.9 33.1 + - - +
743A PHE* 3.0 27.2 - - - +
744A PRO* 3.5 2.5 - - - +
745A GLY* 2.7 38.6 + - - -
746A VAL* 3.0 13.8 + - + +
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Residues in contact with ASP 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A GLU 3.4 5.1 + - - +
668A ASP* 1.3 72.6 + - - +
670A ASN* 1.3 62.9 + - - +
672A MET* 3.7 18.9 - - - +
673A GLU* 3.0 25.8 + - - +
676A ARG* 5.7 0.9 + - - +
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Residues in contact with ASN 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A ASP* 3.0 9.4 + - - +
669A ASP* 1.3 80.0 - - - +
671A LEU* 1.3 57.5 + - - +
673A GLU* 3.5 6.7 + - - +
674A ALA* 3.0 26.9 + - - +
684A LYS* 3.2 21.2 + - - +
688A ASP* 2.8 27.3 + - - -
742A SER* 3.3 20.5 + - - +
743A PHE* 3.2 17.9 - - - -
744A PRO* 5.8 1.1 - - + -
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Residues in contact with LEU 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 3.9 16.2 - - + +
662A LEU* 4.3 9.6 - - + -
663A ALA* 3.7 30.5 - - + +
668A ASP* 2.9 22.3 + - + +
670A ASN* 1.3 73.7 - - - +
672A MET* 1.3 63.9 + - - +
674A ALA* 3.3 3.6 + - + +
675A PHE* 3.2 29.4 + - + -
681A ILE* 3.4 33.0 - - + -
685A THR* 5.8 0.2 - - - +
709A ASN* 6.1 0.4 - - - +
739A TYR* 4.7 6.3 - - - +
743A PHE* 3.8 20.4 - - + -
746A VAL* 4.3 19.1 - - + -
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Residues in contact with MET 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663A ALA* 3.5 24.2 - - - +
667A GLU* 3.5 34.1 - - + +
668A ASP 2.9 16.1 + - - +
669A ASP* 3.7 18.4 - - - +
671A LEU* 1.3 74.1 - - - +
673A GLU* 1.3 60.5 + - - +
675A PHE* 3.4 1.7 + - - -
676A ARG* 2.9 58.7 + - - +
859A ARG* 3.9 28.3 - - - -
860A VAL* 3.7 22.3 - - + +
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Residues in contact with GLU 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A ASP 3.0 19.1 + - - +
670A ASN* 3.7 9.0 - - - +
672A MET* 1.3 73.6 - - - +
674A ALA* 1.3 65.9 + - - +
676A ARG* 3.1 21.1 + - - +
677A ARG* 2.9 74.4 + - - +
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Residues in contact with ALA 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ASN 3.0 15.6 + - - +
671A LEU* 3.4 14.1 - - + +
673A GLU* 1.3 78.6 - - - +
675A PHE* 1.3 58.5 + - - +
677A ARG 3.3 0.9 + - - -
678A ASP 3.1 5.7 + - - -
679A LEU* 3.0 42.9 + - + +
681A ILE* 4.3 14.6 - - + -
684A LYS* 4.3 26.0 - - + +
743A PHE* 5.8 0.2 - - + -
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Residues in contact with PHE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A GLN* 4.2 12.3 - - + -
659A LEU* 3.4 46.7 - - + -
660A ARG* 3.7 54.0 + - + +
663A ALA* 4.1 11.4 - - + -
671A LEU* 3.2 36.9 + - + +
672A MET 4.0 2.9 - - - +
674A ALA* 1.3 77.8 - - - +
676A ARG* 1.3 62.2 + - - +
677A ARG 3.1 2.0 - - - -
678A ASP* 2.9 21.0 + - - +
679A LEU 5.1 7.0 - - - -
681A ILE* 4.0 25.6 - - + -
860A VAL* 4.2 12.6 - - + -
861A PRO* 4.4 7.0 - - - +
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Residues in contact with ARG 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A ASP 5.7 0.6 + - - -
672A MET* 2.9 55.9 + - - +
673A GLU* 3.1 22.1 + - - +
675A PHE* 1.3 77.3 - - - +
677A ARG* 1.3 59.5 + - - +
678A ASP* 3.2 1.3 + - - +
859A ARG* 2.9 33.8 + - - +
860A VAL* 4.9 1.1 - - + -
861A PRO* 4.4 20.3 - - + +
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Residues in contact with ARG 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A GLU* 2.9 54.7 + - - +
674A ALA 3.7 4.9 - - - +
676A ARG* 1.3 76.9 - - + +
678A ASP* 1.3 71.7 + - - +
679A LEU* 3.1 35.6 + - + +
684A LYS* 5.9 2.4 - - - +
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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