Contacts of the helix formed by residues 3665 - 3674 (chain F) 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 PHE3665 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2126F HIS* 4.9 2.0 - + - -
2129F TYR* 3.5 40.4 + + + +
2130F ASP* 3.5 34.5 - - + -
2132F LEU* 5.9 8.1 - - + -
2133F GLY 6.0 1.6 - - - -
3663F HIS* 3.4 28.9 - + + -
3664F SER* 1.3 76.0 - - - +
3666F GLU* 1.3 64.4 + - - +
3667F ASP* 3.2 4.5 + - - -
3668F ARG* 3.8 4.5 + - + +
3669F MET* 3.4 20.7 + - + +
3724F ILE* 3.6 33.2 - - + -
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Residues in contact with GLU3666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3664F SER* 3.1 7.0 - - - +
3665F PHE* 1.3 78.0 - - - +
3667F ASP* 1.3 63.3 + - - +
3670F ILE* 3.4 13.7 + - - +
3724F ILE* 3.2 38.3 - - + +
3727F LYS* 3.9 21.5 - - + -
3728F SER* 3.2 21.1 - - - +
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Residues in contact with ASP3667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3664F SER 4.3 5.1 + - - +
3665F PHE* 3.2 1.2 - - - -
3666F GLU* 1.3 79.4 - - - +
3668F ARG* 1.3 66.0 + - - +
3669F MET 3.1 1.4 + - - -
3670F ILE* 3.3 11.3 + - - +
3671F ASP* 2.7 32.3 + - - +
3728F SER* 4.5 10.6 - - - +
3731F LEU 6.0 3.9 - - - -
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Residues in contact with ARG3668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2129F TYR* 3.4 20.5 + - - +
3665F PHE* 3.8 5.0 + - - +
3667F ASP* 1.3 83.7 - - - +
3669F MET* 1.3 59.1 + - - +
3670F ILE 3.3 0.6 + - - -
3671F ASP* 3.8 8.9 - - - +
3672F ASP* 3.6 23.6 + - - +
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Residues in contact with MET3669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2125F LEU* 6.0 3.9 - - + +
2129F TYR* 3.6 26.0 + - + -
3665F PHE* 3.4 19.6 + - + +
3666F GLU 4.4 4.0 - - - +
3667F ASP 3.1 1.4 + - - -
3668F ARG* 1.3 79.8 - - - +
3670F ILE* 1.3 63.2 - - + +
3672F ASP* 4.5 1.2 - - - +
3673F LEU* 3.4 24.3 + - - +
3724F ILE* 4.4 15.3 - - + -
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Residues in contact with ILE3670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3666F GLU 3.4 18.6 - - - +
3667F ASP 3.3 5.9 + - - +
3669F MET* 1.3 83.1 - - + +
3671F ASP* 1.3 64.9 + - - +
3673F LEU* 3.5 6.2 + - + +
3674F SER* 3.1 23.0 + - - -
3694F LEU* 3.9 23.0 - - + +
3721F TYR* 6.3 3.1 - - + -
3724F ILE* 4.7 9.0 - - + +
3725F MET* 4.4 26.5 - - + -
3728F SER* 3.6 20.9 - - - +
3764F ARG* 3.6 28.5 - - - +
3765F LEU* 5.5 3.8 - - + -
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Residues in contact with ASP3671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3667F ASP* 2.7 38.5 + - - +
3668F ARG* 3.8 7.0 + - - +
3670F ILE* 1.3 77.8 - - - +
3672F ASP* 1.3 57.7 + - - +
3674F SER 3.1 3.5 + - - -
3675F LYS* 2.9 30.2 + - - +
3764F ARG* 3.5 33.9 + - - +
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Residues in contact with ASP3672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104F VAL* 4.6 13.1 - - + +
3668F ARG 3.6 16.8 + - - +
3669F MET* 5.0 1.3 - - - +
3671F ASP* 1.3 79.5 - - - +
3673F LEU* 1.3 60.1 + - - +
3674F SER 3.5 0.2 + - - -
3675F LYS* 3.6 17.0 + - - +
3676F ALA 4.9 0.7 + - - -
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Residues in contact with LEU3673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104F VAL* 4.1 24.2 - - + +
2107F ALA* 5.6 4.0 - - + -
2122F PHE* 5.3 9.9 - - + -
2125F LEU* 4.4 25.8 - - + -
3669F MET 3.4 20.7 + - - +
3670F ILE* 3.5 7.3 + - + +
3671F ASP 3.2 1.0 - - - -
3672F ASP* 1.3 79.5 - - - +
3674F SER* 1.3 58.5 + - - +
3675F LYS 3.5 0.2 - - - -
3676F ALA 5.2 0.2 + - - -
3693F PRO* 3.2 40.3 - - + +
3694F LEU* 3.8 24.8 + - + -
3697F LEU* 3.9 26.5 - - + -
3721F TYR* 5.4 2.9 - - + -
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Residues in contact with SER3674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3670F ILE 3.1 17.1 + - - -
3671F ASP 3.4 3.4 - - - -
3673F LEU* 1.3 75.5 - - - +
3675F LYS* 1.3 65.8 + - - +
3676F ALA 3.6 3.4 - - - -
3692F ASP* 5.2 5.5 - - - +
3693F PRO* 5.2 2.9 - - - -
3694F LEU* 3.6 35.3 + - - +
3764F ARG* 4.9 13.7 + - - +
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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