Contacts of the helix formed by residues 2070 - 2078 (chain A) in PDB entry 4ZWJ
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 GLN2070 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 5.2 7.4 - - + -
2068A TYR 4.4 0.3 - - - +
2069A GLY* 1.3 74.8 - - - -
2071A GLU* 1.3 64.1 + - - +
2072A ASP* 3.5 2.2 - - + +
2073A ILE* 3.4 33.3 - - + +
2074A ASP* 3.4 23.7 + - - +
2141A GLY 5.3 9.8 + - - +
2143A SER* 5.6 0.4 - - - -
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Residues in contact with GLU2071 (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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2067A ARG* 5.0 15.7 + - - +
2069A GLY 5.1 2.9 - - - +
2070A GLN* 1.3 75.0 - - - +
2072A ASP* 1.3 72.3 + - - +
2074A ASP* 4.4 2.2 - - - +
2075A VAL* 3.5 24.9 + - - +
2081A ARG* 6.3 3.6 - - - +
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Residues in contact with ASP2072 (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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67A LYS* 4.6 17.0 - - + +
312A GLN* 3.8 25.7 + - + +
2070A GLN* 3.5 1.4 - - + +
2071A GLU* 1.3 86.9 - - - +
2073A ILE* 1.3 67.7 + - + +
2075A VAL* 3.6 6.5 + - - +
2076A MET* 3.4 19.9 + - - +
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Residues in contact with ILE2073 (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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67A LYS 4.3 3.1 - - - +
70A THR* 3.3 38.8 - - + +
72A LEU* 3.7 31.9 - - + -
73A ASN* 4.6 7.0 - - - +
145A ASN* 5.6 2.9 - - - +
312A GLN* 3.5 26.2 - - - +
2069A GLY* 5.4 2.5 - - - -
2070A GLN* 3.4 33.4 - - + +
2072A ASP* 1.3 76.6 - - + +
2074A ASP* 1.3 73.7 + - + +
2076A MET* 3.2 2.6 + - - +
2077A GLY* 3.1 20.8 + - - -
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Residues in contact with ASP2074 (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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138A VAL* 6.2 0.2 - - - +
139A VAL* 5.2 5.7 - - - +
145A ASN* 5.7 0.4 - - - +
2068A TYR* 3.8 28.8 + - - +
2069A GLY* 5.5 0.4 - - - -
2070A GLN 3.4 17.2 + - - +
2071A GLU* 4.4 2.7 - - - +
2072A ASP 3.4 0.6 - - - -
2073A ILE* 1.3 86.9 - - + +
2075A VAL* 1.3 66.2 + - + +
2076A MET 3.3 0.2 + - - -
2077A GLY* 3.7 6.0 + - - +
2078A LEU 4.3 1.6 + - - -
2079A THR 2.9 33.5 - - - +
2080A PHE* 3.2 1.1 - - - +
2081A ARG* 2.7 36.7 + - - +
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Residues in contact with VAL2075 (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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311A LYS* 3.8 35.8 - - + +
2071A GLU 3.5 16.6 + - - +
2072A ASP* 3.6 7.3 + - - +
2073A ILE 3.4 0.2 - - - -
2074A ASP* 1.3 78.4 - - + +
2076A MET* 1.3 62.2 + - - +
2078A LEU 4.3 10.9 + - - +
2079A THR* 5.0 1.0 - - - -
2080A PHE* 3.8 25.6 - - + +
2081A ARG* 5.9 4.3 - - - +
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Residues in contact with MET2076 (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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310A ASN* 2.8 35.6 - - - +
311A LYS* 4.1 13.4 + - - +
312A GLN* 3.4 32.8 - - + +
313A PHE* 5.9 0.4 - - + -
2072A ASP 3.4 4.3 + - - +
2073A ILE 3.2 9.6 + - - +
2074A ASP 3.1 0.6 - - - -
2075A VAL* 1.3 81.0 - - - +
2077A GLY* 1.3 68.5 + - - +
2078A LEU* 3.5 0.7 + - - -
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Residues in contact with GLY2077 (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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135A ARG* 3.6 38.8 + - - -
257A TYR* 4.1 7.1 + - - -
310A ASN* 4.6 2.4 + - - -
2073A ILE 3.1 13.8 + - - -
2074A ASP 3.7 2.7 + - - -
2075A VAL 3.5 0.6 - - - -
2076A MET* 1.3 79.4 - - - +
2078A LEU* 1.3 64.1 + - - +
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Residues in contact with LEU2078 (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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135A ARG* 5.3 8.5 - - + +
223A TYR* 5.2 6.7 - - + -
226A LEU* 3.4 42.4 - - + -
246A ALA* 4.9 1.2 - - - +
249A GLU* 5.0 8.5 - - - +
250A VAL* 3.5 51.3 + - + +
253A MET* 3.9 23.0 - - + +
254A VAL* 4.3 9.0 - - + -
257A TYR* 4.2 12.3 - - + +
2074A ASP 4.3 2.4 + - - -
2075A VAL 4.5 7.5 - - - +
2076A MET 3.5 1.0 + - - -
2077A GLY* 1.3 81.5 - - - +
2079A THR* 1.3 62.7 + - + +
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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