Contacts of the helix formed by residues 682 - 695 (chain 1) 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 HIS 682 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6791 ILE 3.4 7.1 + - - -
6811 PRO* 1.3 73.5 - - - +
6831 LEU* 1.3 65.0 + - - +
6841 ARG 3.1 3.4 - - - -
6851 SER* 2.7 17.1 + - - +
6861 LEU* 2.9 11.3 + - - -
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Residues in contact with LEU 683 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6791 ILE 3.8 5.9 + - - -
6801 LEU* 3.1 13.2 + - - +
6811 PRO 3.0 4.6 - - - -
6821 HIS* 1.3 76.8 - - - +
6841 ARG* 1.3 64.7 + - - +
6861 LEU* 3.1 1.6 + - - +
6871 VAL* 3.0 22.3 + - - -
7231 SER* 6.2 0.7 - - - -
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Residues in contact with ARG 684 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6811 PRO 4.2 4.4 + - - -
6821 HIS 3.1 1.2 - - - -
6831 LEU* 1.3 76.6 - - - +
6851 SER* 1.3 62.9 + - - +
6871 VAL* 3.4 1.4 + - - +
6881 GLU* 2.9 18.4 + - - -
7231 SER* 5.2 17.1 - - - +
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Residues in contact with SER 685 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6821 HIS* 2.7 14.6 + - - +
6841 ARG* 1.3 70.1 - - - +
6861 LEU* 1.3 53.3 + - - +
6881 GLU* 2.6 26.2 + - - +
6891 ILE 2.9 9.5 + - - -
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Residues in contact with LEU 686 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6821 HIS 2.9 11.7 + - - -
6831 LEU* 3.6 3.4 - - - +
6851 SER* 1.3 72.5 - - - +
6871 VAL* 1.3 65.1 + - - +
6891 ILE* 2.7 14.6 + - - -
6901 ILE* 3.1 8.5 + - - -
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Residues in contact with VAL 687 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6831 LEU 3.0 12.4 + - - -
6841 ARG 3.8 2.9 - - - -
6861 LEU* 1.3 73.6 - - - +
6881 GLU* 1.3 54.6 + - - +
6901 ILE* 2.5 25.1 + - - +
6911 GLU* 3.0 12.6 + - - -
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Residues in contact with GLU 688 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6841 ARG 2.9 11.6 + - - -
6851 SER* 2.6 16.8 + - - +
6871 VAL* 1.3 67.5 - - - +
6891 ILE* 1.3 65.5 + - - +
6911 GLU* 4.6 1.3 + - - +
6921 HIS 5.1 0.7 + - - -
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Residues in contact with ILE 689 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6491 LYS* 5.7 9.0 - - - +
6851 SER 2.9 5.7 + - - -
6861 LEU 2.7 11.1 + - - -
6871 VAL 3.1 0.7 - - - -
6881 GLU* 1.3 81.9 - - - +
6901 ILE* 1.3 62.0 + - - +
6911 GLU 3.0 2.3 + - - -
6921 HIS* 3.3 11.1 + - - -
6931 GLY 4.8 0.5 + - - -
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Residues in contact with ILE 690 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6861 LEU 3.1 6.7 + - - -
6871 VAL* 2.5 14.4 + - - +
6891 ILE* 1.3 70.4 - - - +
6911 GLU* 1.3 64.0 + - - +
6921 HIS 3.2 0.4 - - - -
6931 GLY* 3.0 15.0 + - - +
6941 LEU 4.0 2.1 + - - -
7051 SER* 5.6 5.5 - - - -
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Residues in contact with GLU 691 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6871 VAL 3.0 11.1 + - - -
6881 GLU 4.6 0.8 + - - -
6891 ILE 3.0 1.0 + - - -
6901 ILE* 1.3 77.1 - - - +
6921 HIS* 1.3 57.3 + - - +
6931 GLY 2.7 7.4 + - - -
6941 LEU* 2.9 14.6 + - - -
6951 VAL 4.3 2.3 + - - -
7271 VAL* 6.3 2.9 - - - +
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Residues in contact with HIS 692 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6881 GLU 5.1 0.4 + - - -
6891 ILE 3.3 9.6 + - - -
6901 ILE 3.1 2.0 + - - -
6911 GLU* 1.3 73.5 - - - +
6931 GLY* 1.3 61.3 + - - +
6951 VAL* 4.3 3.6 + - - -
6961 ASP* 4.7 3.6 + - - -
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Residues in contact with GLY 693 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6891 ILE 4.8 0.4 + - - -
6901 ILE 3.0 10.3 + - - -
6911 GLU 2.7 2.8 + - - -
6921 HIS* 1.3 76.8 - - - +
6941 LEU* 1.3 52.1 + - - -
6951 VAL 2.5 18.6 + - - -
6961 ASP* 2.5 21.2 + - - -
7011 VAL 5.0 7.7 - - - -
7021 ARG* 4.7 8.4 + - - -
7051 SER* 6.2 2.0 - - - -
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Residues in contact with LEU 694 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6901 ILE 4.0 2.8 + - - -
6911 GLU* 2.9 10.8 + - - +
6931 GLY* 1.3 74.0 - - - +
6951 VAL* 1.3 58.9 + - - +
6961 ASP 3.3 2.4 + - - +
7021 ARG* 4.4 20.3 - - - +
7051 SER* 6.0 2.0 - - - +
7061 ALA 5.9 2.7 - - - +
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Residues in contact with VAL 695 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6911 GLU 4.3 2.2 + - - -
6921 HIS 4.3 3.7 + - - -
6931 GLY 2.5 7.1 + - - -
6941 LEU* 1.3 72.9 - - - +
6961 ASP* 1.3 65.0 + - - +
6971 GLU* 3.7 0.5 + - - -
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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