Contacts of the helix formed by residues 433 - 440 (chain B) in PDB entry 6HYI
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 433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392B ILE* 4.0 11.1 - - - +
398B GLY* 5.6 0.3 - - - -
400B TRP 3.7 15.4 - - - +
401B LEU* 4.6 2.9 - - - -
432B ILE* 1.3 74.1 - - - +
434B GLU* 1.3 62.8 + - - +
436B GLU* 3.4 10.3 + - - +
437B PHE* 3.6 23.0 - - - -
602B NOS 3.0 24.0 + - - -
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Residues in contact with GLU 434 (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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401B LEU* 3.6 24.5 - - + +
431B HIS* 2.7 41.2 + - + +
432B ILE* 3.5 6.0 + - - -
433B GLY* 1.3 80.6 + - - +
435B LEU* 1.3 87.1 + - + +
436B GLU 3.3 0.2 - - - -
437B PHE* 3.0 9.5 + - - +
438B LEU* 3.0 39.0 + - + +
463B PHE* 4.6 2.7 - - + -
474B LEU* 4.3 19.7 - - + +
477B CYS* 5.4 0.3 - - - +
483B TYR* 3.6 13.7 + - - -
602B NOS 4.2 3.7 + - - -
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Residues in contact with LEU 435 (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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433B GLY 3.3 1.6 - - - -
434B GLU* 1.3 96.6 - - + +
436B GLU* 1.3 65.3 + - - +
438B LEU* 3.2 9.0 + - + +
439B ASN 3.0 20.1 + - - -
441B HIS* 3.6 2.7 + - - -
477B CYS* 3.7 30.3 - - + -
483B TYR* 3.9 12.6 - - + -
486B TYR* 3.6 51.9 + - + -
602B NOS 3.3 46.9 + - + +
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Residues in contact with GLU 436 (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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397B GLU 4.6 0.2 - - - +
398B GLY* 4.2 18.5 - - - +
433B GLY* 3.4 11.4 - - - +
435B LEU* 1.3 76.8 - - - +
437B PHE* 1.3 57.5 + - - +
440B ASN* 2.9 29.3 + - - -
441B HIS* 3.1 42.4 + - - +
442B ARG 3.6 2.7 - - - +
443B THR* 3.4 32.7 - - + +
444B VAL* 3.6 2.8 + - - +
460B ARG* 3.4 6.0 + - - -
602B NOS 2.6 54.3 + - - -
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Residues in contact with PHE 437 (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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398B GLY 2.9 34.8 - - - -
399B GLU* 3.3 24.7 - - - -
400B TRP 3.4 12.8 - - - -
401B LEU* 3.6 23.1 - - + -
433B GLY 3.6 15.3 - - - -
434B GLU* 3.0 8.4 + - - +
436B GLU* 1.3 76.6 - - + +
438B LEU* 1.3 64.8 + - - +
440B ASN* 3.9 11.4 + - - +
458B LEU* 4.5 1.3 - - + -
459B ASN 4.7 0.7 - - - -
460B ARG* 3.5 36.7 + - + +
463B PHE* 3.6 49.6 - + + -
500B VAL* 5.6 2.6 - - - +
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Residues in contact with LEU 438 (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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434B GLU* 3.0 27.6 + - + +
435B LEU* 3.2 14.1 + - + +
437B PHE* 1.3 78.8 - - - +
439B ASN* 1.3 73.8 + - - +
440B ASN* 3.6 6.6 + - - -
463B PHE* 3.8 21.5 - - + -
471B ILE* 3.8 35.0 - - + +
474B LEU* 3.9 35.4 - - + +
475B LYS* 4.3 22.4 + - + +
477B CYS* 5.0 2.5 - - - -
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Residues in contact with ASN 439 (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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435B LEU* 3.0 5.5 + - - +
438B LEU* 1.3 93.3 - - - +
440B ASN* 1.3 73.9 + - - +
441B HIS* 3.5 13.8 + - + +
475B LYS* 4.7 6.2 + - - -
477B CYS* 5.5 3.8 - - - -
486B TYR* 2.8 39.7 + - - +
487B GLN* 5.8 0.4 - - - +
490B LEU* 3.9 14.8 - - + +
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Residues in contact with ASN 440 (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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436B GLU 2.9 12.1 + - - -
437B PHE 3.9 8.5 + - - +
438B LEU 4.6 6.1 + - - -
439B ASN* 1.3 81.7 - - - +
441B HIS* 1.3 57.8 + - - +
460B ARG* 3.0 18.5 + - - -
497B PRO* 3.3 9.9 - - - +
498B SER 3.0 25.7 + - - +
499B TYR* 3.6 35.7 + - + +
500B VAL* 4.6 5.2 + - - +
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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