Contacts of the helix formed by residues 532 - 542 (chain B) in PDB entry 6AHU
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 ASP 532 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B LEU* 4.6 8.9 - - + +
531B GLN* 1.3 87.3 - - - +
533B ASN* 1.3 65.6 + - - +
534B GLU 3.4 2.5 - - - +
535B LYS* 3.9 42.6 + - + +
536B VAL* 3.3 23.6 + - - +
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Residues in contact with ASN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B CYS 5.7 2.5 - - - +
531B GLN 3.6 2.4 - - - -
532B ASP* 1.3 77.1 - - - +
534B GLU* 1.3 66.3 + - + +
536B VAL* 3.5 7.2 + - - +
537B ARG* 3.5 40.9 + - - +
106G GLU* 5.9 1.2 - - - +
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Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B ASP* 3.4 1.0 - - - +
533B ASN* 1.3 79.6 - - + +
535B LYS* 1.3 66.7 + - + +
537B ARG* 3.7 8.2 + - - +
538B GLN* 3.4 21.0 + - - +
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Residues in contact with LYS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B LEU* 3.3 36.5 - - + +
532B ASP* 3.7 37.3 + - + +
533B ASN 3.3 0.6 - - - -
534B GLU* 1.3 79.0 - - + +
536B VAL* 1.3 64.1 + - - +
538B GLN* 3.5 24.6 + - - +
539B LEU* 3.7 3.5 + - - +
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B LEU* 3.8 22.0 - - + -
492B GLY* 5.0 12.3 - - - +
493B ILE* 4.4 23.5 - - + +
531B GLN 5.2 2.5 - - - +
532B ASP 3.3 16.8 - - - +
533B ASN* 3.5 10.2 + - - +
534B GLU 3.4 0.4 - - - -
535B LYS* 1.3 76.4 - - - +
537B ARG* 1.3 62.5 + - - +
539B LEU* 3.2 6.9 + - - +
540B LEU* 3.1 41.6 + - + +
22G LEU* 4.7 10.3 - - + -
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Residues in contact with ARG 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B ASN* 3.5 35.7 + - - +
534B GLU* 4.1 7.1 - - - +
535B LYS 3.4 0.4 - - - -
536B VAL* 1.3 78.4 - - - +
538B GLN* 1.3 61.5 + - - +
540B LEU* 3.9 10.8 - - + +
541B LEU* 3.2 47.5 + - + +
86F ARG* 6.0 2.0 - - - +
106G GLU* 3.0 43.5 + - + +
124G ILE* 4.9 7.6 - - + -
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Residues in contact with GLN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B GLU 3.4 11.7 + - - +
535B LYS* 3.6 20.4 - - - +
536B VAL 3.2 0.6 - - - -
537B ARG* 1.3 79.3 - - - +
539B LEU* 1.3 58.3 + - - +
541B LEU* 5.6 0.2 - - - -
542B GLU* 3.7 24.7 + - + +
543B GLY 3.7 4.9 + - - -
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B ILE* 4.0 32.1 - - + +
489B LEU* 4.9 8.3 - - + -
490B LEU* 4.5 6.7 - - + -
493B ILE* 3.8 28.7 - - + -
499B ILE* 4.2 25.5 - - + +
500B PRO* 4.8 1.6 - - - +
503B THR* 6.2 0.2 - - - +
505B LEU* 5.6 3.1 - - + -
535B LYS 3.7 6.8 + - - +
536B VAL* 3.2 8.7 + - - +
538B GLN* 1.3 79.0 - - - +
540B LEU* 1.3 64.7 + - + +
541B LEU 3.5 0.2 - - - -
543B GLY* 3.3 33.6 - - - +
544B VAL 5.1 1.3 - - - +
545B PRO* 5.1 13.5 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ILE* 5.4 11.2 - - + -
498B GLU* 3.3 51.0 - - + +
499B ILE* 5.3 4.0 - - + +
500B PRO* 4.8 14.5 - - - +
536B VAL* 3.1 41.3 + - + +
537B ARG* 3.6 7.8 + - + +
539B LEU* 1.3 81.8 - - + +
541B LEU* 1.3 64.4 + - + +
542B GLU 4.9 0.2 - - - -
22G LEU* 4.1 17.3 - - + -
106G GLU* 5.8 7.2 - - + -
108G VAL* 3.5 29.4 - - + +
122G THR* 5.5 0.2 - - - +
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PRO* 5.9 1.2 - - - +
537B ARG* 3.2 37.8 + - + +
538B GLN 5.0 0.2 - - - +
540B LEU* 1.3 79.0 - - + +
542B GLU* 1.3 73.4 + - + +
108G VAL* 3.8 26.0 - - + -
122G THR* 3.0 36.6 + - - +
123G ARG 4.0 15.7 - - - +
124G ILE* 3.8 29.8 - - + -
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PRO* 5.1 6.4 - - - +
538B GLN* 3.7 16.4 + - + +
540B LEU 4.9 0.2 - - - -
541B LEU* 1.3 89.4 - - + +
543B GLY* 1.3 67.0 + - - +
544B VAL* 3.5 26.0 - - + +
122G THR* 4.9 8.9 + - - +
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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