Contacts of the helix formed by residues 441 - 446 (chain B) in PDB entry 4AQD
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 441 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.3 20.3 - - - +
223B GLN* 3.1 31.6 + - - +
224B SER* 4.3 3.4 + - - -
322B ASN* 2.8 28.5 + - - +
419B TYR* 4.3 11.9 - - + +
421B PHE* 3.6 39.5 - - + -
439B GLY* 3.3 11.6 + - - -
440B TYR* 1.3 72.7 - - - +
442B ILE* 1.3 71.8 + - - +
443B GLU 3.3 2.9 - - - -
444B PHE* 3.1 15.5 + - - +
445B VAL* 3.1 17.2 + - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TRP* 4.2 12.1 - - + -
112B TRP* 4.2 3.8 - - + -
127B VAL* 3.4 26.0 - - + +
128B TYR* 3.8 27.4 - - + +
197B GLU* 3.7 33.7 - - + +
223B GLN* 4.4 3.6 - - - +
439B GLY* 3.2 22.1 + - - +
441B GLU* 1.3 94.4 - - - +
443B GLU* 1.3 58.0 + - - +
445B VAL* 3.1 7.4 + - - +
446B PHE* 3.0 42.9 + - + -
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 4.5 4.9 - - - +
82B TRP* 5.9 0.3 - - - -
127B VAL* 4.5 10.6 - - + +
425B SER* 3.7 1.4 + - - -
439B GLY 5.0 1.0 - - - +
440B TYR* 3.5 33.1 - - - +
442B ILE* 1.3 80.3 - - - +
444B PHE* 1.3 75.8 + - + +
446B PHE 3.9 0.6 - - - -
447B GLY 3.2 4.2 + - - -
448B LEU* 3.0 50.6 + - + -
449B PRO* 3.3 3.4 - - - +
456B TYR* 2.6 28.6 + - + +
1531B PEG 2.2 40.7 + - - +
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 4.2 11.0 - + + -
423B HIS* 3.6 27.4 - + - -
425B SER* 4.0 19.1 - - - -
440B TYR 3.9 14.1 - - - -
441B GLU 3.1 8.0 + - - +
443B GLU* 1.3 96.0 - - + +
445B VAL* 1.3 63.7 + - - +
447B GLY 3.4 1.0 + - - -
449B PRO* 4.2 8.1 - - + -
456B TYR* 4.5 3.1 - + - -
460B GLU* 3.7 40.8 - - + -
463B LEU* 4.1 18.2 - - + -
464B SER* 2.6 42.0 + - - +
467B ILE* 4.0 17.2 - - + +
468B VAL* 3.6 5.9 - - - +
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Residues in contact with VAL 445 (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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133B LEU* 3.7 11.3 - - + +
195B PHE* 3.9 17.7 - - + -
223B GLN* 3.8 22.4 - - - +
441B GLU* 3.1 18.0 + - + +
442B ILE* 3.1 9.1 + - - +
444B PHE* 1.3 77.1 - - - +
446B PHE* 1.3 61.7 + - + +
447B GLY 3.2 0.4 - - - -
467B ILE* 3.9 20.4 - - + -
468B VAL* 3.2 19.2 - - - +
471B TRP* 3.5 45.0 - - + +
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Residues in contact with PHE 446 (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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112B TRP* 3.4 57.7 - + + -
127B VAL 3.3 20.6 - - - +
128B TYR* 3.2 25.4 - - - -
129B ASP 3.5 20.6 - - - +
130B GLY* 4.2 9.9 - - - -
132B PHE* 3.4 23.0 - - - +
133B LEU* 4.3 16.1 + - + -
141B VAL* 4.9 3.6 - - + -
195B PHE* 3.9 15.7 - + - -
442B ILE* 3.0 30.4 + - + +
445B VAL* 1.3 81.0 - - + +
447B GLY* 1.3 61.4 + - - +
448B LEU* 3.5 13.1 + - + -
468B VAL* 4.5 1.3 - - - -
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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