Contacts of the helix formed by residues 467 - 475 (chain C) in PDB entry 5I94
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 PHE 467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C MET* 3.0 15.4 + - + +
465C TYR 2.9 1.6 + - - -
466C ASP* 1.3 77.9 - - - +
468C SER* 1.3 63.8 + - - +
469C GLY 3.3 2.0 - - - -
470C GLN* 3.1 31.7 + - + +
471C PHE* 2.9 51.6 + + + +
474C HIS* 5.8 1.3 - + - -
505C ASP* 5.9 1.3 - - - -
507C MET* 4.0 26.1 - - + -
509C ASN* 3.4 20.6 - - - +
514C ILE* 4.4 13.7 - - + -
518C HIS* 4.0 23.6 - + - -
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Residues in contact with SER 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C HIS 4.3 4.1 - - - +
461C SER* 3.1 27.1 - - - -
462C CYS* 3.3 5.2 - - - -
463C GLY 3.2 8.9 + - - -
464C MET* 3.1 26.2 + - - -
465C TYR 2.8 20.0 + - - -
466C ASP 3.3 1.6 - - - -
467C PHE* 1.3 77.6 - - - +
469C GLY* 1.3 57.9 + - - +
471C PHE* 3.7 2.0 - - - +
472C ALA* 2.8 30.8 + - - +
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Residues in contact with GLY 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 6.2 0.6 - - - +
461C SER 5.7 0.2 - - - -
466C ASP 4.6 1.4 + - - -
467C PHE 3.3 0.6 - - - -
468C SER* 1.3 80.5 - - - +
470C GLN* 1.3 64.1 + - - +
472C ALA* 3.8 5.6 - - - +
473C PHE* 3.1 24.3 + - - +
310D LYS* 4.5 5.1 - - - +
311D GLU* 3.3 31.7 + - - -
312D PRO* 5.4 5.4 - - - -
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Residues in contact with GLN 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C ASP 5.8 1.3 - - - +
467C PHE* 3.1 38.8 + - + +
469C GLY* 1.3 77.9 - - - +
471C PHE* 1.3 57.5 + - - +
473C PHE* 4.7 0.4 - - - -
474C HIS* 2.9 45.6 + - + +
310D LYS* 2.9 39.3 - - - +
311D GLU* 3.5 20.7 + - + +
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Residues in contact with PHE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C MET 5.8 0.9 - - - -
460C HIS 5.3 4.5 - - - -
464C MET* 3.7 20.9 - - + -
467C PHE* 2.9 29.1 + + + +
468C SER 3.7 3.4 - - - +
470C GLN* 1.3 75.7 - - - +
472C ALA* 1.3 60.9 + - - +
473C PHE 3.2 0.2 - - - -
475C VAL* 2.8 66.9 + - + +
476C GLY 3.1 5.2 + - - -
477C LEU 3.3 26.9 - - - -
479C ALA* 3.7 24.0 - - + -
487C ILE* 5.6 0.2 - - + -
489C LEU* 4.4 1.6 - - + -
514C ILE* 3.9 31.0 - - + -
517C CYS* 4.1 18.4 - - + -
518C HIS* 4.6 0.7 - + - -
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Residues in contact with ALA 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C HIS* 3.8 38.5 + - + +
461C SER* 5.3 2.2 - - - -
468C SER 2.8 20.6 + - - +
469C GLY* 3.8 7.0 - - - +
471C PHE* 1.3 74.8 - - - +
473C PHE* 1.3 63.3 + - - +
476C GLY* 3.2 23.9 - - - +
477C LEU 5.4 0.4 - - - +
527C HIS* 3.8 3.8 + - - -
457D SER* 4.7 3.6 + - - -
461D SER* 6.6 0.4 - - - -
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Residues in contact with PHE 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C GLY 3.1 17.5 + - - +
470C GLN 3.8 3.8 - - - +
471C PHE 3.2 0.2 - - - -
472C ALA* 1.3 76.3 - - - +
474C HIS* 1.3 90.4 + + + +
527C HIS* 2.9 23.7 + - - -
292D TYR* 3.8 16.4 - - - -
301D THR* 4.0 12.3 - - + -
305D HIS* 3.8 8.1 - - - -
310D LYS* 3.5 31.4 - - + +
453D ARG* 5.7 1.0 + - - -
454D ASN* 3.6 42.3 - - - +
457D SER* 4.2 12.7 + - - -
458D LEU* 3.8 28.5 - - + -
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Residues in contact with HIS 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C PHE* 5.8 1.3 - + - -
470C GLN* 2.9 37.6 + - + +
473C PHE* 1.3 97.0 - + - +
475C VAL* 1.3 62.0 + - + +
518C HIS* 4.1 26.6 - + + +
521C VAL* 4.2 8.8 - - - +
527C HIS* 3.7 8.5 - - - -
301D THR* 5.3 4.9 - - + -
310D LYS* 3.1 37.6 + - - -
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C PHE* 2.8 52.8 + - + +
474C HIS* 1.3 73.8 - - + +
476C GLY* 1.3 68.3 + - - +
477C LEU* 3.3 16.2 + - + +
489C LEU* 5.0 0.7 - - + -
517C CYS* 3.6 15.7 - - + +
518C HIS* 3.6 33.9 - - + +
521C VAL* 3.6 36.0 - - + +
527C HIS* 3.5 11.3 - - - -
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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