Contacts of the helix formed by residues 4038 - 4046 (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 GLN4038 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3976F ALA* 4.6 23.6 - - + +
3981F TRP* 5.6 2.9 - - - +
4034F MET* 2.9 27.4 + - - +
4035F ILE* 3.3 15.3 - - + +
4036F ALA 3.1 1.4 - - - -
4037F ARG* 1.3 84.9 + - - +
4039F MET* 1.3 72.7 + - - +
4040F VAL 3.3 0.4 - - - -
4041F ASP* 3.2 17.5 + - - +
4042F MET* 3.3 13.2 + - - +
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Residues in contact with MET4039 (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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4022F LEU* 4.0 31.6 - - + +
4025F LEU* 3.7 30.7 - - + -
4026F LEU* 3.7 20.9 - - + -
4035F ILE 3.3 24.5 - - - +
4036F ALA* 3.5 20.6 + - - +
4038F GLN* 1.3 82.0 - - - +
4040F VAL* 1.3 61.5 + - - +
4042F MET* 3.2 15.0 + - - +
4043F LEU* 3.3 21.7 + - + +
4145F LEU* 4.2 21.3 - - + -
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Residues in contact with VAL4040 (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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4036F ALA 4.3 6.5 - - - +
4037F ARG* 3.3 31.6 - - + +
4039F MET* 1.3 75.9 - - - +
4041F ASP* 1.3 63.0 + - + +
4042F MET 3.3 0.2 - - - -
4043F LEU* 3.7 11.2 + - - +
4044F VAL* 3.7 18.2 + - - +
4145F LEU* 4.2 24.5 - - + +
4149F VAL* 3.8 29.8 - - + -
4152F ASP* 5.4 9.0 - - + -
4154F ARG* 5.1 6.2 - - + +
4155F LEU* 5.5 4.9 - - + +
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Residues in contact with ASP4041 (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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4037F ARG 3.7 12.3 - - - +
4038F GLN* 3.2 17.6 + - - +
4039F MET 3.2 0.6 - - - -
4040F VAL* 1.3 82.3 - - + +
4042F MET* 1.3 60.7 + - - +
4043F LEU 3.4 0.4 - - - -
4044F VAL* 3.8 16.2 + - - +
4045F GLU* 4.3 9.5 + - - +
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Residues in contact with MET4042 (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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3981F TRP* 5.0 20.0 - - + +
3984F VAL* 5.8 5.6 - - + -
3985F VAL* 5.4 5.2 - - + +
4022F LEU* 6.5 1.3 - - + -
4038F GLN 3.3 10.6 + - - +
4039F MET* 3.2 13.2 + - - +
4041F ASP* 1.3 76.4 - - - +
4043F LEU* 1.3 56.1 + - + +
4044F VAL 3.3 1.1 - - - -
4045F GLU* 3.9 4.6 + - - +
4046F SER* 2.5 34.1 + - - -
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Residues in contact with LEU4043 (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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4039F MET* 3.3 17.6 + - + +
4040F VAL* 3.7 10.7 + - - +
4041F ASP 3.4 0.6 - - - -
4042F MET* 1.3 81.7 - - + +
4044F VAL* 1.3 51.7 + - - +
4046F SER* 3.3 10.5 - - - +
4047F SER* 2.6 34.5 + - - -
4050F VAL* 5.0 12.9 - - + +
4145F LEU* 4.3 23.3 - - + -
4154F ARG* 4.9 12.8 - - + +
4155F LEU* 5.4 4.9 - - - -
4158F PHE* 3.9 28.5 - - + -
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Residues in contact with VAL4044 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4040F VAL 3.7 16.4 - - - +
4041F ASP* 3.8 10.2 + - - +
4042F MET 3.3 0.8 - - - -
4043F LEU* 1.3 78.3 - - - +
4045F GLU* 1.3 65.0 + - + +
4047F SER* 2.7 20.6 + - - +
4154F ARG* 4.4 17.9 - - + -
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Residues in contact with GLU4045 (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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100D THR* 5.7 5.0 - - - +
3985F VAL* 4.8 19.2 - - + +
4041F ASP 4.3 8.9 + - - +
4042F MET* 3.9 6.1 + - - +
4044F VAL* 1.3 83.0 - - + +
4046F SER* 1.3 57.4 + - - +
4047F SER 3.3 1.5 + - - -
4048F SER* 4.6 2.6 + - - -
4049F ASN* 3.4 11.4 + - - -
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Residues in contact with SER4046 (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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3985F VAL* 4.3 16.8 - - - -
3988F LEU* 5.5 6.5 - - - -
4042F MET 2.5 23.9 + - - -
4043F LEU* 3.3 12.7 - - - +
4045F GLU* 1.3 75.7 - - - +
4047F SER* 1.3 56.3 + - - +
4048F SER 3.3 2.7 - - - -
4049F ASN* 3.0 17.2 + - - +
4050F VAL* 2.7 49.8 + - - +
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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