Contacts of the helix formed by residues 432 - 447 (chain C) in PDB entry 5A31
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 ASP 432 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C ARG* 3.6 25.0 + - - -
399C TYR* 4.4 3.6 - - - -
426C HIS* 4.5 1.9 - - - -
429C ARG* 3.5 34.2 + - + +
430C PRO 3.3 2.6 - - - -
431C ASN* 1.3 75.7 - - - +
433C SER* 1.3 67.6 + - - +
434C ARG* 3.0 38.6 + - - +
435C MET* 3.5 30.6 + - - +
436C LEU* 3.6 15.9 + - - +
462C VAL* 4.4 0.9 - - - -
465C VAL* 5.5 4.2 - - - +
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Residues in contact with SER 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ASN 3.1 6.8 + - - -
432C ASP* 1.3 77.0 + - - +
434C ARG* 1.3 59.1 + - - +
436C LEU* 3.0 8.1 + - - +
437C VAL* 2.9 33.1 + - - +
459C ALA* 3.7 6.5 + - - +
462C VAL* 3.5 19.3 - - - -
463C GLY* 4.7 0.4 - - - -
464C ASP* 3.3 44.7 + - - -
465C VAL* 4.3 9.8 + - - -
466C GLU* 5.5 0.8 + - - -
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Residues in contact with ARG 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 3.7 45.8 - - - +
399C TYR* 4.8 1.6 + - - -
403C TYR* 4.4 6.1 + - + +
432C ASP* 3.0 23.6 + - - +
433C SER* 1.3 73.8 - - - +
435C MET* 1.3 65.4 + - - +
437C VAL* 3.5 9.7 + - - +
438C ALA* 3.1 21.3 + - - +
465C VAL* 5.0 5.5 - - + +
466C GLU* 3.8 34.5 + - - +
44R HIS* 3.9 25.1 + - - -
46R ASP* 3.7 24.4 + - - +
49R ILE* 3.5 47.7 + - + +
52R ARG* 5.2 2.8 - - - -
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Residues in contact with MET 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TYR* 3.5 32.3 - - + -
403C TYR* 3.4 34.8 - - + -
422C TYR* 4.7 5.4 - - + +
425C ALA* 4.0 10.8 - - + +
426C HIS* 3.9 39.9 - - + +
429C ARG* 4.9 2.7 - - - +
432C ASP* 3.5 28.9 + - + +
433C SER 3.3 0.4 - - - -
434C ARG* 1.3 76.9 - - - +
436C LEU* 1.3 65.6 + - - +
438C ALA* 3.0 7.8 + - - +
439C LEU* 2.9 25.8 + - - +
49R ILE* 3.6 15.9 - - + -
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 5.6 3.8 - - + -
426C HIS* 3.3 36.3 - - + +
430C PRO 4.2 3.1 - - - +
432C ASP 3.6 13.4 + - - +
433C SER 3.0 6.6 + - - +
435C MET* 1.3 77.0 - - - +
437C VAL* 1.3 62.8 + - - +
439C LEU* 3.3 14.3 + - + +
440C GLY 3.0 17.8 + - - -
455C CYS* 3.5 29.9 - - - +
458C ARG* 3.8 42.0 - - + +
459C ALA* 4.0 4.7 - - + +
462C VAL* 3.9 22.7 - - + -
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C SER* 2.9 25.8 + - - +
434C ARG* 3.6 11.9 - - - +
436C LEU* 1.3 75.0 - - - +
438C ALA* 1.3 58.8 + - - +
440C GLY* 3.3 2.8 + - - -
441C GLU* 3.0 40.4 + - - +
456C TYR* 3.8 11.7 - - + -
459C ALA* 3.7 16.6 - - + -
464C ASP* 4.4 5.8 - - - +
466C GLU* 6.0 4.3 - - + -
468C MET* 5.5 5.8 - - + -
469C ALA* 4.1 15.9 - - + +
472C LYS* 4.5 17.7 - - + -
52R ARG* 4.8 9.4 - - + +
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C TYR* 4.3 3.6 - - + -
422C TYR* 3.9 26.2 - - + -
434C ARG 3.1 12.9 + - - +
435C MET 3.0 9.4 + - - +
437C VAL* 1.3 75.7 - - - +
439C LEU* 1.3 66.0 + - - +
441C GLU* 3.1 4.6 + - - +
442C CYS* 3.0 25.1 + - - -
52R ARG* 3.2 35.1 + - - +
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 5.2 6.1 - - + -
419C LEU* 3.4 30.1 - - + -
422C TYR* 4.1 18.7 - - + -
423C ARG* 4.2 20.0 - - + -
426C HIS* 4.0 35.2 - - + +
435C MET 2.9 14.8 + - - +
436C LEU* 3.5 18.2 - - + +
438C ALA* 1.3 74.5 - - - +
440C GLY* 1.3 57.7 + - - +
442C CYS* 3.2 5.7 + - - +
443C TYR* 2.9 42.2 + - + +
455C CYS* 3.6 13.9 - - - -
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LEU 3.0 11.6 + - - -
437C VAL 3.6 4.7 - - - -
438C ALA 3.2 0.2 - - - -
439C LEU* 1.3 75.8 - - - +
441C GLU* 1.3 52.7 + - - +
443C TYR 3.4 0.2 + - - -
444C GLU* 2.8 30.0 + - - +
452C ALA* 3.6 10.1 - - - +
455C CYS* 3.7 19.7 - - - +
456C TYR* 3.3 25.0 + - - -
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Residues in contact with GLU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLU* 3.5 14.2 - - - +
437C VAL* 3.0 16.6 + - - +
438C ALA 3.1 9.8 + - - +
440C GLY* 1.3 75.1 - - - +
442C CYS* 1.3 59.1 + - - +
444C GLU* 3.4 7.0 + - - +
445C LYS* 3.1 41.6 + - - +
456C TYR* 3.4 7.5 + - - +
472C LYS* 3.1 34.1 + - - +
52R ARG* 3.2 46.5 + - - +
57R TRP* 5.1 4.2 - - - -
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Residues in contact with CYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLU* 4.1 10.1 - - - -
415C PRO* 3.9 25.0 - - + +
418C CYS* 3.8 18.8 - - - -
419C LEU* 4.5 15.7 - - + -
422C TYR* 3.8 26.9 - - - -
438C ALA 3.0 16.1 + - - +
439C LEU* 3.2 7.8 + - - +
441C GLU* 1.3 74.7 - - - +
443C TYR* 1.3 60.0 + - - +
445C LYS* 3.0 5.6 + - - +
446C LEU* 2.9 30.9 + - - +
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Residues in contact with TYR 443 (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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167A LYS* 3.9 8.3 + - - -
168A ASP 4.6 0.5 + - - -
169A TYR* 4.2 11.8 - - - -
217A LEU* 4.1 13.7 - - + +
419C LEU* 3.9 31.7 - - + +
423C ARG* 4.1 13.9 - - - +
439C LEU* 2.9 37.7 + - + +
440C GLY* 3.8 4.0 - - - +
442C CYS* 1.3 75.7 - - - +
444C GLU* 1.3 56.9 + - - +
446C LEU* 3.4 6.6 + - + +
447C ASN 2.9 22.5 + - - -
448C GLN* 3.0 31.0 + - + +
451C GLU* 3.6 38.1 - - + -
452C ALA 3.8 14.6 - - - +
455C CYS* 3.7 24.9 - - - -
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLY 2.8 18.1 + - - +
441C GLU* 3.4 7.9 - - - +
443C TYR* 1.3 76.6 - - - +
445C LYS* 1.3 62.6 + - + +
447C ASN* 3.2 14.2 + - - +
449C LEU* 4.4 11.2 - - + +
452C ALA* 3.8 8.2 - - + +
456C TYR* 3.0 19.0 + - - +
472C LYS* 4.6 9.5 + - - +
475C LYS* 5.9 2.9 - - - +
476C LEU* 3.6 30.9 + - + +
479C GLN* 5.0 9.6 - - - +
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Residues in contact with LYS 445 (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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410C GLU* 3.2 39.9 + - + +
413C LYS* 6.1 3.3 - - - +
415C PRO* 4.1 28.7 - - + +
441C GLU* 3.1 28.8 + - - +
442C CYS* 3.0 7.6 + - - +
444C GLU* 1.3 75.1 - - + +
446C LEU* 1.3 64.1 + - - +
447C ASN* 3.4 2.4 + - - +
57R TRP* 6.0 0.8 - - - -
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 5.5 0.2 - - - +
415C PRO* 4.0 10.5 - - + -
416C PHE* 3.5 43.1 - - + +
419C LEU* 3.7 29.4 - - + -
442C CYS 2.9 13.7 + - - +
443C TYR* 3.5 10.8 - - + +
445C LYS* 1.3 75.3 - - - +
447C ASN* 1.3 68.3 + - - +
448C GLN* 3.5 29.9 + - + +
322O LEU* 3.9 33.2 - - + +
326O GLU* 4.2 4.7 - - - +
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Residues in contact with ASN 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C TYR 2.9 4.0 + - - -
444C GLU 3.2 13.5 + - - +
445C LYS 3.2 3.1 - - - +
446C LEU* 1.3 79.7 - - - +
448C GLN* 1.3 60.1 + - - +
449C LEU* 3.4 29.2 + - - +
479C GLN* 5.1 2.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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