Contacts of the helix formed by residues 461 - 471 (chain A) in PDB entry 3AF5
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 MET 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLN* 5.2 9.4 - - - +
290A LEU* 4.2 27.6 - - + +
294A ASP* 4.0 25.8 - - + +
297A GLU* 5.8 4.3 - - - +
432A ALA* 4.1 6.5 - - + +
460A GLY* 1.3 78.3 - - - +
462A ILE* 1.3 63.6 + - - +
463A TRP* 3.2 4.0 - - - +
464A GLU* 3.3 17.4 + - + +
465A ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ALA 4.4 2.5 - - - +
432A ALA* 3.9 26.2 - - - +
436A ALA* 3.8 22.4 - - + -
437A GLN* 3.7 1.0 - - - +
440A MET* 4.0 21.1 - - - -
458A LEU* 4.3 15.9 - - + -
459A ASP 3.5 15.0 - - - +
460A GLY 3.1 5.1 - - - +
461A MET* 1.3 78.4 - - - +
463A TRP* 1.3 52.2 + - - +
465A ALA* 3.4 3.1 + - - +
466A THR* 2.5 36.8 + - - +
519A ILE* 3.4 46.4 - - + +
520A ALA* 3.9 5.6 - - - -
521A SER 4.0 4.3 - - - +
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Residues in contact with TRP 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.5 39.0 - - + +
440A MET* 4.5 5.4 - - + -
458A LEU* 3.4 33.2 + - + +
461A MET* 3.2 1.5 - - + +
462A ILE* 1.3 79.0 - - - +
464A GLU* 1.3 68.2 + - - +
466A THR* 3.1 16.5 + - + -
467A ALA* 2.9 23.5 + - + +
492A PHE 3.6 26.0 - - - -
493A LEU* 4.7 5.4 - - - -
494A SER 5.3 1.6 - - - -
497A PHE* 4.4 9.9 - - + -
499A PRO* 3.7 36.8 - - + +
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Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLN 4.3 2.4 - - - +
150A SER* 2.5 30.3 + - - -
151A GLN* 3.2 35.8 + - + +
152A THR* 2.8 22.6 + - - +
290A LEU* 3.7 25.4 - - + -
461A MET* 3.3 30.7 + - + +
463A TRP* 1.3 81.4 - - - +
465A ALA* 1.3 63.3 + - - +
467A ALA* 3.1 13.2 + - - +
468A ILE* 3.2 11.3 + - - +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU* 4.3 1.3 - - + +
290A LEU* 3.7 13.5 - - + -
432A ALA 3.4 26.9 - - - +
433A VAL* 3.7 22.4 - - + -
437A GLN* 3.7 3.4 - - - +
461A MET 3.0 15.0 + - - +
462A ILE 3.6 0.9 - - - +
464A GLU* 1.3 76.5 - - - +
466A THR* 1.3 59.4 + - - +
468A ILE* 2.9 26.2 + - - +
469A HIS* 3.0 16.8 + - + -
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Residues in contact with THR 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.4 7.2 - - + -
437A GLN* 3.5 10.5 + - + +
440A MET* 3.8 20.3 - - + +
462A ILE* 2.5 23.3 + - - +
463A TRP* 3.2 16.7 - - + -
465A ALA* 1.3 73.8 - - - +
467A ALA* 1.3 64.6 + - - +
469A HIS* 3.0 24.6 + - - +
470A THR* 3.3 8.0 + - - +
492A PHE* 3.4 44.4 - - + -
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.0 26.8 - - + +
149A GLN 4.0 10.5 - - - +
150A SER* 4.0 19.4 - - - -
463A TRP* 2.9 13.6 + - + +
464A GLU* 3.1 14.3 + - - +
466A THR* 1.3 76.4 - - - +
468A ILE* 1.3 62.8 + - - +
470A THR* 2.7 26.4 + - - -
471A ALA* 3.4 8.1 + - - +
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Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 3.6 13.9 - - - +
152A THR* 4.1 15.3 - - - -
153A ILE* 4.5 10.5 - - + -
283A PRO 4.7 0.2 - - - +
286A ASP* 4.1 30.1 - - + +
287A LEU* 3.9 31.4 - - + -
290A LEU* 4.1 14.6 - - + -
346A LEU* 3.9 3.3 - - + +
464A GLU* 3.4 15.5 - - - +
465A ALA* 2.9 9.9 + - - +
467A ALA* 1.3 76.8 - - - +
469A HIS* 1.3 59.9 + - - +
471A ALA* 3.3 5.0 + - - +
472A TYR* 3.2 39.9 - - + -
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Residues in contact with HIS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU* 4.6 1.6 - - + -
345A ILE* 6.0 0.2 - - - +
346A LEU* 3.6 42.3 + - + +
375A LEU* 3.9 20.4 - - + +
433A VAL* 4.0 21.1 - - + +
434A GLY 5.2 0.4 + - - -
437A GLN* 3.5 41.1 + - + +
465A ALA 3.0 24.3 + - - -
466A THR 3.0 9.9 + - - +
468A ILE* 1.3 77.2 - - - +
470A THR* 1.3 56.7 + - - +
471A ALA 3.0 0.2 - - - -
472A TYR* 3.0 26.7 + - - +
473A PRO 3.8 0.2 - - - -
476A LEU* 3.7 18.3 - - + +
492A PHE* 4.3 16.2 - + + -
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Residues in contact with THR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO* 4.2 1.6 - - - +
147A PRO* 3.4 39.4 - - + +
148A LEU* 3.8 30.0 + - + +
466A THR 3.7 8.1 - - - +
467A ALA 2.7 19.8 + - - -
469A HIS* 1.3 75.1 - - - +
471A ALA* 1.3 58.1 + - - +
472A TYR 3.3 0.2 - - - -
473A PRO* 3.8 10.0 - - - +
476A LEU* 5.4 0.4 - - - -
484A ILE* 4.4 11.5 - - + +
485A PHE* 6.0 0.5 - - - +
490A ASN* 4.1 7.6 - - - +
492A PHE* 3.5 31.0 - - + -
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 5.9 3.1 - - - +
146A PRO* 4.2 20.4 - - + -
148A LEU 5.6 0.2 - - - +
150A SER* 6.0 0.2 - - - -
153A ILE* 3.5 31.2 - - + -
467A ALA 3.4 5.8 + - - +
468A ILE 3.3 7.1 + - - +
469A HIS 3.0 1.0 - - - -
470A THR* 1.3 77.8 + - - +
472A TYR* 1.3 71.7 + - + +
473A PRO* 3.3 9.6 - - - +
474A GLU* 4.2 2.1 - - - +
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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