Contacts of the helix formed by residues 2131 - 2138 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1952B LEU* 5.7 0.2 - - - +
1955B ARG* 5.6 4.3 + - - -
2043B CYS* 3.6 26.1 + - - -
2127B ARG 4.7 2.9 - - - -
2128B GLN 4.7 1.9 + - - -
2129B TYR 4.0 2.6 + - - -
2130B ASP* 1.3 74.5 - - - +
2132B LEU* 1.3 61.0 + - - +
2133B GLY 3.4 0.4 - - - -
2134B GLU* 3.3 6.5 + - - +
2135B LEU* 2.9 32.4 + - - +
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Residues in contact with LEU2132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2039B LEU* 5.6 1.8 - - + -
2040B LEU* 5.3 13.0 - - + -
2043B CYS* 3.8 15.7 - - + -
2045B ILE* 5.3 8.5 - - + -
2130B ASP* 3.7 0.8 - - - +
2131B GLY* 1.3 77.4 - - - +
2133B GLY* 1.3 58.3 + - - +
2135B LEU* 3.2 24.8 - - + +
2136B LEU* 2.9 30.1 + - - +
3658B ILE* 4.8 11.8 - - + +
3661B GLU* 4.0 17.9 - - + +
3662B ASP* 5.1 1.1 - - - -
3663B HIS* 3.8 37.2 - - + +
3665B PHE* 5.9 6.3 - - + -
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Residues in contact with GLY2133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2130B ASP* 4.7 7.1 - - - +
2131B GLY* 3.4 2.0 - - - +
2132B LEU* 1.3 77.5 - - - +
2134B GLU* 1.3 57.4 + - - +
2136B LEU* 3.3 12.1 + - - +
2137B ARG* 2.9 30.8 + - - +
3665B PHE* 6.0 2.0 - - - -
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Residues in contact with GLU2134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952B LEU* 3.6 26.1 - - + +
2127B ARG* 5.1 14.1 - - + +
2130B ASP 3.9 15.8 + - - +
2131B GLY* 3.3 10.9 + - - +
2132B LEU 3.2 0.6 - - - -
2133B GLY* 1.3 75.5 - - - +
2135B LEU* 1.3 57.7 + - - +
2137B ARG* 3.3 6.2 + - - +
2138B ALA* 2.9 28.6 + - - +
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Residues in contact with LEU2135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952B LEU* 4.7 4.6 - - + +
1955B ARG* 4.6 18.4 - - - +
1956B VAL* 5.8 4.9 - - + -
1959B LEU* 5.7 9.4 - - + -
2039B LEU* 4.4 17.9 - - + -
2043B CYS* 3.7 18.2 - - - -
2131B GLY 2.9 20.3 + - - +
2132B LEU* 3.2 27.1 - - + +
2134B GLU* 1.3 76.1 - - - +
2136B LEU* 1.3 63.2 + - - +
2138B ALA* 3.5 12.7 + - - +
2139B LEU* 3.2 27.0 + - + +
3653B TYR* 6.0 0.4 - - + -
3658B ILE* 4.1 32.8 - - + -
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Residues in contact with LEU2136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132B LEU 2.9 17.7 + - - +
2133B GLY* 3.6 11.0 - - - +
2134B GLU 3.2 0.2 - - - -
2135B LEU* 1.3 79.8 - - - +
2137B ARG* 1.3 66.9 + - + +
2139B LEU* 3.4 24.7 + - + +
2140B PRO* 3.6 8.7 - - - +
3654B LYS* 6.1 3.6 - - + -
3658B ILE* 4.0 19.7 - - + +
3659B LEU* 3.8 29.8 - - + -
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Residues in contact with ARG2137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2133B GLY 2.9 17.3 + - - +
2134B GLU* 3.8 5.2 - - - +
2136B LEU* 1.3 83.4 - - + +
2138B ALA* 1.3 60.5 + - - +
2139B LEU 3.2 0.2 - - - -
2140B PRO* 3.4 14.0 - - - +
2141B ARG* 4.6 5.2 + - - +
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Residues in contact with ALA2138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734B TYR* 4.5 12.1 - - + -
1952B LEU* 4.1 24.2 - - + -
1956B VAL* 4.1 15.8 - - + +
2134B GLU 2.9 16.9 + - - +
2135B LEU* 3.9 8.1 - - - +
2136B LEU 3.2 0.6 - - - -
2137B ARG* 1.3 76.1 - - - +
2139B LEU* 1.3 64.3 + - - +
2140B PRO 3.6 0.2 - - - -
2141B ARG* 3.7 8.6 + - - +
2142B ALA* 3.3 22.0 + - - +
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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