Contacts of the helix formed by residues 2070 - 2081 (chain A) in PDB entry 6AH0
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 LYS2070 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2068A SER 3.0 8.3 + - - -
2069A SER* 1.3 78.9 - - - +
2071A THR* 1.3 64.3 + - - +
2072A GLU 3.3 0.2 - - - -
2073A TRP* 3.2 11.3 + - - -
2074A ARG* 3.7 6.6 + - - -
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Residues in contact with THR2071 (chain A).
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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2068A SER 5.0 1.0 - - - -
2070A LYS* 1.3 72.7 - - - +
2072A GLU* 1.3 62.9 + - - +
2074A ARG* 3.0 13.3 + - - +
2075A VAL* 3.1 12.1 + - - -
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Residues in contact with GLU2072 (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 PHE* 5.7 2.7 - - - +
2068A SER* 4.6 17.8 - - - +
2069A SER 4.7 1.4 - - - +
2070A LYS 3.3 2.8 - - - +
2071A THR* 1.3 76.2 - - - +
2073A TRP* 1.3 62.1 + - - +
2074A ARG 3.6 0.2 + - - -
2075A VAL* 4.0 1.2 + - - +
2076A ARG* 3.7 13.3 + - - -
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Residues in contact with TRP2073 (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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2069A SER* 4.8 6.8 - - - +
2070A LYS 3.2 12.1 + - - +
2071A THR 3.1 1.0 - - - -
2072A GLU* 1.3 80.0 - - - +
2074A ARG* 1.3 55.7 + - - +
2076A ARG* 3.6 1.4 + - - -
2077A ALA* 3.0 23.7 + - - -
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Residues in contact with ARG2074 (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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2070A LYS 3.7 6.2 + - - -
2071A THR* 3.0 6.2 + - - +
2073A TRP* 1.3 74.3 - - - +
2075A VAL* 1.3 68.3 + - - +
2077A ALA* 3.0 11.5 + - - +
2078A ILE* 3.0 13.3 + - - -
1047D PRO* 5.8 9.1 - - - +
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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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2071A THR 3.1 13.2 + - - -
2072A GLU* 4.0 1.7 + - - +
2073A TRP 3.5 0.2 - - - -
2074A ARG* 1.3 75.6 - - - +
2076A ARG* 1.3 57.3 + - - +
2078A ILE* 4.0 0.5 - - - -
2079A SER* 3.0 23.7 + - - -
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Residues in contact with ARG2076 (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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2072A GLU 3.7 8.9 + - - -
2073A TRP 3.6 5.5 + - - -
2074A ARG 3.2 0.2 - - - -
2075A VAL* 1.3 75.5 - - - +
2077A ALA* 1.3 57.8 + - - +
2079A SER* 3.7 2.2 - - - +
2080A ALA* 2.9 25.8 + - - -
2120A LEU 6.0 0.3 + - - -
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Residues in contact with ALA2077 (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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2073A TRP 3.0 13.5 + - - -
2074A ARG* 3.0 8.1 + - - +
2076A ARG* 1.3 78.6 - - - +
2078A ILE* 1.3 64.2 + - - +
2079A SER 3.5 0.2 + - - -
2080A ALA* 3.6 7.0 + - - +
2081A ALA* 3.7 8.1 + - - -
2305A TYR* 6.4 2.0 - - - +
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Residues in contact with ILE2078 (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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2074A ARG 3.0 12.7 + - - -
2075A VAL 4.1 0.4 - - - -
2077A ALA* 1.3 74.1 - - - +
2079A SER* 1.3 68.5 + - - +
2081A ALA* 3.7 8.0 + - - +
2082A ASN 4.5 1.0 + - - -
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Residues in contact with SER2079 (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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2075A VAL 3.0 16.8 + - - -
2076A ARG* 3.7 4.5 - - - +
2077A ALA 3.2 0.2 - - - -
2078A ILE* 1.3 77.9 - - - +
2080A ALA* 1.3 51.2 + - - +
2081A ALA 3.0 0.4 - - - -
2082A ASN* 2.8 30.3 + - - -
2083A LEU 4.2 0.5 + - - -
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Residues in contact with ALA2080 (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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2076A ARG 2.9 18.6 + - - -
2077A ALA 3.6 2.8 + - - -
2078A ILE 3.5 0.2 - - - -
2079A SER* 1.3 70.9 - - - +
2081A ALA* 1.3 56.1 + - - +
2082A ASN 3.0 1.3 - - - -
2083A LEU* 2.9 23.7 + - - +
2084A HIS 4.9 0.2 + - - -
2116A CYS 4.9 7.8 - - - +
2118A SER 5.2 9.1 - - - +
2119A ASP* 5.9 4.5 - - - +
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Residues in contact with ALA2081 (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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2077A ALA 3.7 10.4 + - - -
2078A ILE* 3.7 6.0 + - - +
2079A SER 2.8 2.4 + - - -
2080A ALA* 1.3 75.0 - - - +
2082A ASN* 1.3 56.6 + - - +
2083A LEU 3.6 0.2 - - - -
2084A HIS 5.0 1.4 + - - -
1008D THR 4.6 11.1 - - - +
1010D SER* 5.6 9.3 + - - +
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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