Contacts of the helix formed by residues 435 - 443 (chain C) in PDB entry 4QGC
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 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432C THR* 2.8 24.5 + - - +
433C LYS 3.5 1.2 - - - -
434C SER* 1.3 78.2 - - - +
436C ARG* 1.3 62.7 + - - +
437C SER 3.2 3.1 - - - -
438C ALA* 3.1 5.6 + - - +
439C HIS* 3.0 40.5 + - - -
459C THR* 4.3 8.7 - - - -
463C ALA* 6.3 1.3 - - - -
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Residues in contact with ARG 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C SER* 3.1 33.6 + - - +
435C GLY* 1.3 76.4 - - - +
437C SER* 1.3 62.2 + - - +
439C HIS* 3.2 14.9 + - + +
440C GLN* 3.2 36.1 + - - +
1002C SO4 3.6 11.8 + - - +
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Residues in contact with SER 437 (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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409C THR* 5.0 2.0 - - - +
430C VAL* 3.3 16.8 - - - +
431C LEU 4.8 0.9 - - - -
432C THR* 4.1 2.9 - - - -
436C ARG* 1.3 76.6 - - - +
438C ALA* 1.3 62.3 + - - +
440C GLN* 3.4 21.1 + - - +
441C VAL* 3.3 19.9 - - - +
512C LEU* 5.1 2.6 - - - +
522C THR* 3.3 38.9 - - - +
1002C SO4 3.0 21.3 + - - -
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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
----------------------------------------------------------
430C VAL* 3.9 15.5 - - + +
432C THR* 4.4 8.7 + - + -
435C GLY* 3.1 10.5 + - - +
437C SER* 1.3 78.3 - - - +
439C HIS* 1.3 63.6 + - + +
441C VAL* 3.4 4.4 + - - +
442C ALA* 3.1 17.3 + - - +
450C ILE* 4.4 6.0 - - + +
452C ALA* 3.9 28.9 - - + -
463C ALA* 6.1 0.9 - - + -
469C ILE* 3.4 23.0 - - + +
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Residues in contact with HIS 439 (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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266C LYS* 4.7 15.5 - - + -
321C GLY 5.0 3.2 - - - +
434C SER 4.6 4.9 - - - -
435C GLY* 3.0 34.8 + - - -
436C ARG* 3.2 14.2 + - + +
438C ALA* 1.3 79.3 - - + +
440C GLN* 1.3 57.7 + - - +
442C ALA* 3.2 5.6 + - - +
443C ARG* 3.1 24.9 + - - +
459C THR 5.5 0.6 + - - -
462C GLN* 5.2 3.6 - - + -
463C ALA* 4.5 13.2 + - + +
466C TYR* 3.2 61.9 + + + +
469C ILE* 4.0 11.9 - - + -
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Residues in contact with GLN 440 (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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407C ASP* 4.7 1.9 - - - +
409C THR* 3.3 39.2 - - + +
410C GLU* 3.3 27.9 + - - +
413C ALA* 4.0 8.5 - - + +
436C ARG* 3.2 29.4 + - - +
437C SER* 3.4 18.3 - - - +
439C HIS* 1.3 76.2 - - - +
441C VAL* 1.3 59.8 + - - +
443C ARG* 3.8 11.6 + - - +
444C TYR* 3.1 29.5 - - - -
1002C SO4 5.9 0.2 + - - -
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Residues in contact with VAL 441 (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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413C ALA* 4.0 17.5 - - + +
416C ALA* 5.2 0.7 - - + -
417C VAL* 3.9 17.8 - - + +
428C ILE* 4.2 18.2 - - + -
430C VAL* 4.2 7.0 - - + -
437C SER 3.3 15.7 - - - +
438C ALA* 3.4 8.2 + - - +
439C HIS 3.2 0.4 - - - -
440C GLN* 1.3 76.7 - - - +
442C ALA* 1.3 62.8 + - - +
444C TYR* 3.3 16.5 + - - +
446C PRO* 3.7 10.2 - - - +
450C ILE* 3.7 21.5 - - + -
512C LEU* 3.7 28.3 - - + -
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Residues in contact with ALA 442 (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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438C ALA 3.1 14.0 + - - +
439C HIS* 3.2 10.0 + - - +
441C VAL* 1.3 76.2 - - - +
443C ARG* 1.3 63.2 + - - +
445C ARG* 3.1 31.7 + - - +
446C PRO* 4.4 1.3 - - - +
450C ILE* 3.5 11.8 - - + +
466C TYR* 4.4 9.4 - - + -
467C ARG 4.0 11.0 - - - +
469C ILE* 3.7 26.5 - - + -
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Residues in contact with ARG 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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318C ASN 4.0 8.7 - - - +
319C ARG* 3.2 19.4 + - - +
320C ALA 4.2 4.5 - - - -
321C GLY* 3.5 35.9 - - - +
398C LEU* 3.2 37.2 + - + +
401C LEU* 5.7 6.5 - - - +
410C GLU* 3.3 13.3 + - - +
439C HIS 3.1 11.7 + - - +
440C GLN* 3.8 14.0 + - - +
441C VAL 3.2 0.4 - - - -
442C ALA* 1.3 76.4 - - - +
444C TYR* 1.3 97.9 + - + +
445C ARG* 3.2 10.2 + - - +
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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