Contacts of the helix formed by residues 967 - 982 (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 GLU 967 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9621 MET* 3.6 20.2 + - - +
9651 CYS 3.5 2.2 - - - -
9661 GLN* 1.3 74.2 - - - +
9681 GLU* 1.3 61.8 + - - +
9691 LYS 3.6 1.8 - - - -
9701 LEU* 3.4 12.7 + - - -
9711 MET 3.5 6.9 + - - -
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Residues in contact with GLU 968 (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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9661 GLN* 3.6 6.2 + - - +
9671 GLU* 1.3 70.1 - - - +
9691 LYS* 1.3 59.4 + - - +
9701 LEU 2.9 2.0 - - - -
9711 MET* 2.4 26.9 + - - +
9721 GLY 2.7 11.1 + - - -
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Residues in contact with LYS 969 (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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9671 GLU 3.6 0.4 - - - -
9681 GLU* 1.3 73.5 - - - +
9701 LEU* 1.3 56.5 + - - +
9721 GLY* 3.2 3.9 + - - +
9731 HIS* 2.9 26.2 + - - -
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Residues in contact with LEU 970 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9671 GLU 3.4 10.9 + - - -
9681 GLU 2.9 1.2 - - - -
9691 LYS* 1.3 75.6 - - - +
9711 MET* 1.3 56.0 + - - +
9731 HIS* 3.0 4.5 + - - +
9741 LEU* 2.9 26.5 + - - -
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Residues in contact with MET 971 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9671 GLU 3.5 5.6 + - - -
9681 GLU* 2.4 22.2 + - - +
9701 LEU* 1.3 66.2 - - - +
9721 GLY* 1.3 62.8 + - - +
9741 LEU* 4.5 1.1 - - - +
9751 GLY* 3.0 22.6 + - - +
10101 THR* 5.7 4.1 - - - -
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Residues in contact with GLY 972 (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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9681 GLU 2.7 14.6 + - - -
9691 LYS* 3.5 5.4 - - - -
9711 MET* 1.3 69.1 - - - +
9731 HIS* 1.3 69.0 + - - +
9751 GLY* 3.9 0.2 - - - -
9761 VAL* 3.1 18.0 + - - -
10101 THR* 6.0 4.7 - - - -
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Residues in contact with HIS 973 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9691 LYS 2.9 16.5 + - - -
9701 LEU* 3.0 5.1 + - - +
9721 GLY* 1.3 75.1 - - - +
9741 LEU* 1.3 61.9 + - - +
9771 VAL* 2.9 21.0 + - - -
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Residues in contact with LEU 974 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9701 LEU 2.9 16.4 + - - -
9711 MET* 4.3 0.9 - - - +
9731 HIS* 1.3 67.0 - - - +
9751 GLY* 1.3 70.8 + - - +
9781 LEU* 2.9 22.6 + - - +
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Residues in contact with GLY 975 (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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9711 MET 3.0 18.3 + - - -
9721 GLY 3.9 0.2 - - - -
9741 LEU* 1.3 79.2 - - - +
9761 VAL* 1.3 62.4 + - - +
9791 TYR* 3.0 16.3 + - - -
10101 THR* 5.9 2.2 - - - -
10111 PRO* 5.3 12.7 - - - +
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Residues in contact with VAL 976 (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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9721 GLY 3.1 12.6 + - - -
9731 HIS 3.9 0.9 - - - -
9751 GLY* 1.3 77.5 - - - +
9771 VAL* 1.3 58.2 + - - +
9791 TYR* 2.9 16.9 + - - +
9801 GLU* 3.0 10.2 + - - -
10101 THR 6.0 0.8 - - - -
10111 PRO* 5.5 4.9 - - - -
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Residues in contact with VAL 977 (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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9731 HIS 2.9 14.4 + - - -
9761 VAL* 1.3 72.7 - - - +
9781 LEU* 1.3 69.6 + - - +
9801 GLU* 3.2 8.4 + - - +
9811 TYR 3.6 6.4 + - - -
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Residues in contact with LEU 978 (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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9731 HIS 4.5 0.2 + - - -
9741 LEU* 2.9 16.3 + - - +
9771 VAL* 1.3 74.1 - - - +
9791 TYR* 1.3 65.5 + - - +
9801 GLU 2.6 2.3 + - - -
9811 TYR* 2.7 18.5 + - - +
9821 LEU* 3.6 3.1 + - - -
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Residues in contact with TYR 979 (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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9751 GLY 3.0 13.5 + - - -
9761 VAL* 2.9 10.6 + - - +
9781 LEU* 1.3 73.1 - - - +
9801 GLU* 1.3 62.6 + - - +
9821 LEU* 3.4 10.2 + - - -
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Residues in contact with GLU 980 (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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9761 VAL 3.0 10.9 + - - -
9771 VAL* 3.2 4.8 + - - +
9781 LEU 2.6 5.3 + - - -
9791 TYR* 1.3 74.6 - - - +
9811 TYR* 1.3 56.5 + - - +
9821 LEU 2.8 6.6 + - - -
9831 GLY* 3.3 9.9 + - - -
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Residues in contact with TYR 981 (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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9771 VAL 3.6 5.4 + - - -
9781 LEU* 2.7 15.5 + - - +
9801 GLU* 1.3 65.2 - - - +
9821 LEU* 1.3 48.9 + - - +
9831 GLY 2.5 6.4 + - - -
9841 GLU* 2.2 38.6 + - - +
9901 LEU* 5.6 4.2 - - - -
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Residues in contact with LEU 982 (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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9781 LEU 3.6 3.8 + - - -
9791 TYR 3.4 10.0 + - - -
9801 GLU 2.8 4.8 + - - -
9811 TYR* 1.3 74.1 - - - +
9831 GLY* 1.3 56.6 + - - +
9841 GLU 3.4 3.9 - - - +
9901 LEU* 6.0 4.7 - - - +
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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