Contacts of the helix formed by residues 570 - 583 (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 TYR 570 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5671 VAL* 2.7 19.8 + - - +
5691 PRO* 1.3 71.0 - - - +
5711 VAL* 1.3 50.4 + - - -
5721 HIS 3.5 1.3 - - - -
5731 LYS* 2.9 10.4 + - - +
5741 ILE* 2.7 33.1 + - - -
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Residues in contact with VAL 571 (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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5671 VAL 3.4 4.3 + - - -
5681 ARG* 3.0 12.9 + - - +
5691 PRO 3.5 0.8 - - - -
5701 TYR* 1.3 75.8 - - - +
5721 HIS* 1.3 65.7 + - - +
5741 ILE* 2.8 11.9 + - - +
5751 LEU 3.0 10.6 + - - -
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Residues in contact with HIS 572 (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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1291 SER* 5.7 1.8 - - - -
5681 ARG 5.0 0.2 + - - -
5691 PRO 5.2 1.0 + - - -
5711 VAL* 1.3 73.7 - - - +
5731 LYS* 1.3 54.4 + - - +
5741 ILE 2.8 10.4 + - - -
5751 LEU* 3.0 13.0 + - - +
5761 VAL* 3.2 12.0 + - - -
6121 THR* 6.0 6.2 - - - +
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Residues in contact with LYS 573 (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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1291 SER* 4.7 22.2 + - - +
5691 PRO 5.2 1.4 + - - -
5701 TYR* 2.9 15.8 + - - +
5721 HIS* 1.3 73.5 - - - +
5741 ILE* 1.3 57.1 + - - +
5761 VAL* 4.7 1.6 - - - -
5771 VAL 5.2 1.9 + - - -
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Residues in contact with ILE 574 (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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5701 TYR 2.7 11.2 + - - -
5711 VAL* 2.8 5.2 + - - +
5721 HIS 2.8 0.4 + - - -
5731 LYS* 1.3 77.9 - - - +
5751 LEU* 1.3 65.2 + - - +
5761 VAL 3.0 2.2 - - - -
5771 VAL* 2.8 16.1 + - - -
5781 ILE* 3.2 7.3 + - - -
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Residues in contact with LEU 575 (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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5711 VAL 3.0 8.2 + - - -
5721 HIS* 3.0 7.0 + - - +
5741 ILE* 1.3 74.0 - - - +
5761 VAL* 1.3 59.8 + - - +
5781 ILE* 2.8 3.8 + - - +
5791 GLU* 2.7 32.5 + - - +
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Residues in contact with VAL 576 (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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5721 HIS 3.2 11.5 + - - -
5731 LYS* 5.5 1.3 - - - +
5741 ILE 2.9 2.2 + - - -
5751 LEU* 1.3 75.7 - - - +
5771 VAL* 1.3 57.8 + - - +
5791 GLU 4.7 0.5 + - - -
5801 PRO 4.9 3.5 - - - -
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Residues in contact with VAL 577 (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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5391 LEU 5.6 6.5 - - - -
5731 LYS 5.2 2.0 + - - -
5741 ILE 2.8 9.8 + - - -
5761 VAL* 1.3 77.1 - - - +
5781 ILE* 1.3 65.7 + - - +
5791 GLU 3.6 0.2 + - - -
5801 PRO* 3.7 6.9 - - - +
5811 LEU 4.2 2.6 + - - -
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Residues in contact with ILE 578 (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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5741 ILE 3.2 7.9 + - - -
5751 LEU* 2.8 11.8 + - - +
5771 VAL* 1.3 70.4 - - - +
5791 GLU* 1.3 53.0 + - - +
5811 LEU* 2.4 38.5 + - - -
5821 LEU 3.8 0.9 + - - -
5931 GLY* 6.0 2.1 - - - -
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Residues in contact with GLU 579 (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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5751 LEU* 2.7 21.0 + - - +
5781 ILE* 1.3 68.5 - - - +
5801 PRO* 1.3 63.7 - - - +
5821 LEU* 2.7 18.3 + - - +
5831 ILE 3.7 2.1 + - - -
6271 THR* 5.5 12.7 - - - +
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Residues in contact with PRO 580 (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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5751 LEU 4.8 0.4 - - - -
5761 VAL 4.9 3.4 - - - -
5771 VAL 3.7 6.9 - - - +
5781 ILE 2.8 4.6 - - - -
5791 GLU* 1.3 70.7 - - - +
5811 LEU* 1.3 52.2 + - - +
5831 ILE* 2.7 37.7 + - - +
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Residues in contact with LEU 581 (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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5771 VAL 4.2 2.6 + - - -
5781 ILE 2.4 24.0 + - - -
5801 PRO* 1.3 65.8 - - - +
5821 LEU* 1.3 61.0 + - - +
5831 ILE 3.3 0.7 + - - -
5841 ASP* 3.6 11.4 + - - +
5891 ALA* 4.6 5.3 - - - -
5901 ARG* 4.2 16.0 + - - -
5931 GLY* 5.5 8.1 - - - -
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Residues in contact with LEU 582 (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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5781 ILE 3.8 0.8 + - - -
5791 GLU* 2.7 21.0 + - - +
5811 LEU* 1.3 72.2 - - - +
5831 ILE* 1.3 55.4 + - - +
5841 ASP 3.2 7.1 + - - +
5901 ARG* 5.0 10.9 - - - +
5931 GLY* 5.7 2.5 - - - -
5941 ARG 6.3 0.2 - - - +
154G U 4.1 11.2 - - - +
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Residues in contact with ILE 583 (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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5791 GLU 3.7 2.2 + - - -
5801 PRO* 2.7 22.5 + - - +
5821 LEU* 1.3 69.0 - - - +
5841 ASP* 1.3 54.8 + - - +
154G U 4.5 22.2 - - - -
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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