Contacts of the helix formed by residues 2131 - 2138 (chain H) 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 GLY2131 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1955H ARG* 5.6 5.3 + - - -
2043H CYS* 3.6 25.3 + - - -
2127H ARG 4.7 2.5 - - - -
2128H GLN 4.7 2.5 + - - -
2129H TYR 4.0 3.0 + - - -
2130H ASP* 1.3 73.3 - - - +
2132H LEU* 1.3 61.6 + - - +
2133H GLY 3.4 0.7 - - - -
2134H GLU* 3.3 6.4 + - - +
2135H LEU* 2.9 32.4 + - - +
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Residues in contact with LEU2132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2039H LEU* 5.6 1.8 - - + -
2040H LEU* 5.3 13.9 - - + -
2043H CYS* 3.8 15.5 - - + -
2045H ILE* 5.3 9.0 - - + -
2130H ASP 3.7 0.2 - - - -
2131H GLY* 1.3 77.0 - - - +
2133H GLY* 1.3 57.7 + - - +
2135H LEU* 3.2 26.6 - - + +
2136H LEU* 2.9 29.8 + - - +
3658H ILE* 4.8 11.1 - - + +
3661H GLU* 4.0 17.7 - - + +
3662H ASP* 5.1 1.3 - - - -
3663H HIS* 3.8 37.7 - - + +
3665H PHE* 6.0 7.0 - - + -
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Residues in contact with GLY2133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2130H ASP* 4.7 8.0 - - - +
2131H GLY 3.4 1.6 - - - +
2132H LEU* 1.3 78.5 - - - +
2134H GLU* 1.3 57.3 + - - +
2136H LEU* 3.3 13.2 + - - +
2137H ARG* 2.9 30.3 + - - +
3665H PHE* 6.0 2.0 - - - -
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Residues in contact with GLU2134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952H LEU* 3.6 25.7 - - + +
2127H ARG* 5.1 14.1 - - + +
2130H ASP* 3.9 16.7 + - - +
2131H GLY* 3.3 10.8 + - - +
2132H LEU 3.2 0.6 - - - -
2133H GLY* 1.3 76.8 - - - +
2135H LEU* 1.3 58.0 + - - +
2137H ARG* 3.3 6.7 + - - +
2138H ALA* 2.9 28.6 + - - +
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Residues in contact with LEU2135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952H LEU* 4.7 4.7 - - + +
1955H ARG* 4.6 16.8 - - - +
1956H VAL* 5.8 4.7 - - + +
1959H LEU* 5.7 9.9 - - + -
2039H LEU* 4.4 17.7 - - + -
2043H CYS* 3.7 18.8 - - - -
2131H GLY 2.9 20.9 + - - +
2132H LEU* 3.2 26.7 - - + +
2134H GLU* 1.3 76.1 - - - +
2136H LEU* 1.3 63.4 + - - +
2138H ALA* 3.5 13.8 + - - +
2139H LEU* 3.2 26.7 + - + +
3653H TYR* 6.0 0.4 - - + -
3658H ILE* 4.1 32.8 - - + -
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Residues in contact with LEU2136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132H LEU 2.9 18.6 + - - +
2133H GLY* 3.6 11.2 - - - +
2135H LEU* 1.3 80.3 - - - +
2137H ARG* 1.3 66.2 + - + +
2139H LEU* 3.4 24.4 + - + +
2140H PRO* 3.6 9.7 - - - +
3654H LYS* 6.1 3.4 - - + -
3658H ILE* 4.0 20.9 - - + +
3659H LEU* 3.8 29.6 - - + -
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Residues in contact with ARG2137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2133H GLY 2.9 16.7 + - - +
2134H GLU* 3.8 5.6 - - - +
2136H LEU* 1.3 82.3 - - + +
2138H ALA* 1.3 59.6 + - - +
2139H LEU 3.2 0.9 - - - -
2140H PRO* 3.4 14.0 - - - +
2141H ARG* 4.6 4.9 + - - +
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Residues in contact with ALA2138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734H TYR* 4.5 11.5 - - + -
1952H LEU* 4.1 24.0 - - + -
1956H VAL* 4.1 15.2 - - + +
2134H GLU 2.9 16.9 + - - +
2135H LEU* 3.9 8.5 - - - +
2136H LEU 3.2 0.8 - - - -
2137H ARG* 1.3 75.6 - - - +
2139H LEU* 1.3 63.1 + - - +
2140H PRO 3.6 0.4 - - - -
2141H ARG* 3.7 8.1 + - - +
2142H ALA* 3.3 22.5 + - - +
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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