Contacts of the helix formed by residues 527 - 540 (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 GLY 527 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5231 ALA 3.2 16.0 + - - -
5241 ARG* 4.0 7.4 - - - -
5251 GLU 2.9 4.8 - - - -
5261 PHE* 1.3 85.0 - - - +
5281 ALA* 1.3 68.8 + - - +
5291 GLY 3.3 2.4 + - - -
5301 PRO 3.9 0.2 - - - -
5311 LEU* 3.7 9.7 + - - -
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Residues in contact with ALA 528 (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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5231 ALA 4.9 0.2 + - - -
5271 GLY* 1.3 70.6 - - - -
5291 GLY* 1.3 55.0 + - - +
5311 LEU* 2.4 29.4 + - - +
5321 PHE* 3.0 12.5 + - - +
5661 LEU 6.5 1.6 - - - -
5671 VAL* 6.5 1.1 - - - +
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Residues in contact with GLY 529 (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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5271 GLY 3.3 1.8 - - - -
5281 ALA* 1.3 73.4 - - - +
5301 PRO* 1.3 65.6 - - - +
5321 PHE* 5.7 0.2 - - - -
5331 ASN* 3.0 21.7 + - - -
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Residues in contact with PRO 530 (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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5261 PHE 4.6 7.1 - - - +
5271 GLY 3.9 3.9 - - - +
5281 ALA 3.4 0.4 - - - -
5291 GLY* 1.3 75.6 - - - +
5311 LEU* 1.3 65.9 + - - +
5331 ASN* 3.3 2.6 + - - -
5341 GLN* 3.0 13.0 + - - -
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Residues in contact with LEU 531 (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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5271 GLY 3.7 6.6 + - - -
5281 ALA* 2.4 19.0 + - - +
5301 PRO* 1.3 65.5 - - - +
5321 PHE* 1.3 52.6 + - - +
5341 GLN* 2.2 32.1 + - - +
5351 ILE* 2.8 9.6 + - - -
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Residues in contact with PHE 532 (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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5281 ALA 3.0 12.8 + - - -
5291 GLY 4.3 0.2 - - - -
5311 LEU* 1.3 70.4 - - - +
5331 ASN* 1.3 63.5 + - - +
5341 GLN 3.1 0.7 + - - -
5351 ILE* 4.1 3.6 - - - +
5361 LEU* 3.1 25.3 + - - +
5371 PRO 4.8 0.2 - - - -
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Residues in contact with ASN 533 (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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5291 GLY 3.0 15.0 + - - -
5301 PRO* 3.5 6.5 - - - -
5311 LEU 2.9 0.2 + - - -
5321 PHE* 1.3 77.0 - - - +
5341 GLN* 1.3 55.8 + - - +
5361 LEU 4.8 1.4 + - - -
5371 PRO 4.8 4.7 - - - -
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Residues in contact with GLN 534 (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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5301 PRO 3.0 7.4 + - - -
5311 LEU 2.2 23.0 + - - -
5331 ASN* 1.3 69.2 - - - +
5351 ILE* 1.3 59.9 + - - +
5371 PRO* 4.9 1.4 - - - +
5381 LEU* 4.8 2.3 + - - -
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Residues in contact with ILE 535 (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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5311 LEU 2.8 9.1 + - - -
5321 PHE* 3.2 3.1 + - - +
5341 GLN* 1.3 78.2 - - - +
5361 LEU* 1.3 52.9 + - - +
5371 PRO 2.7 2.9 - - - -
5381 LEU* 2.2 40.2 + - - +
5391 LEU 3.1 4.0 + - - -
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Residues in contact with LEU 536 (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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5321 PHE* 3.1 15.6 + - - +
5351 ILE* 1.3 73.1 - - - +
5371 PRO* 1.3 62.8 - - - +
5391 LEU* 3.8 5.7 - - - +
5401 MET* 3.0 18.5 + - - -
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Residues in contact with PRO 537 (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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5321 PHE 4.8 0.8 - - - -
5331 ASN 4.8 6.0 - - - +
5341 GLN 4.9 1.1 - - - +
5351 ILE 2.7 5.2 - - - -
5361 LEU* 1.3 73.2 - - - +
5381 LEU* 1.3 56.1 + - - +
5401 MET* 3.0 15.9 + - - -
5411 SER* 3.0 12.8 + - - -
965 ARG* 5.7 9.2 - - - -
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Residues in contact with LEU 538 (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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5341 GLN 4.8 1.8 + - - -
5351 ILE* 2.2 21.8 + - - +
5371 PRO* 1.3 64.3 - - - +
5391 LEU* 1.3 61.0 + - - +
5401 MET 2.9 4.7 - - - -
5411 SER* 3.0 14.7 + - - +
5441 LEU* 5.6 3.6 - - - -
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Residues in contact with LEU 539 (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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5351 ILE 3.1 9.5 + - - -
5361 LEU* 3.5 6.4 + - - +
5381 LEU* 1.3 77.8 - - - +
5401 MET* 1.3 55.8 + - - +
5411 SER 3.5 0.4 - - - -
5491 ARG* 6.5 1.3 - - - +
5771 VAL* 5.6 6.1 - - - -
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Residues in contact with MET 540 (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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1241 ARG* 6.2 0.2 - - - -
5361 LEU 3.0 12.5 + - - -
5371 PRO 3.3 7.4 - - - -
5381 LEU 2.9 1.0 - - - -
5391 LEU* 1.3 78.2 - - - +
5411 SER* 1.3 63.0 + - - +
5421 PRO* 3.0 5.0 - - - +
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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