Contacts of the helix formed by residues 530 - 541 (chain C) in PDB entry 1G88
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 HIS 530 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B PRO* 3.8 42.1 - - + +
357B SER* 5.0 4.5 + - - -
320C PRO* 3.7 12.4 - - + +
321C GLU 5.4 0.4 + - - -
322C TYR* 3.1 54.9 + + + +
323C TRP 3.0 12.0 + - - +
324C CYS* 3.7 5.2 - - - -
325C SER* 2.4 31.6 + - - -
340C LYS* 5.3 3.6 - - + -
528C HIS* 3.5 14.1 - - + -
529C LEU* 1.3 69.4 - - - +
531C ARG* 1.3 67.8 + - - +
533C LEU* 2.8 14.9 + - - +
534C GLN* 3.0 13.9 + - - +
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Residues in contact with ARG 531 (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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315C SER* 3.1 24.7 + - - -
317C HIS* 2.8 37.8 + - - +
318C PRO 3.3 12.0 + - - -
319C ALA* 4.1 4.6 - - - +
320C PRO* 3.5 19.2 - - + +
323C TRP* 4.5 4.6 + - + +
394C GLU* 2.7 62.5 + - + +
395C GLY* 4.7 6.3 - - - -
440C LEU* 4.0 10.8 - - + -
529C LEU* 3.7 0.6 - - - +
530C HIS* 1.3 76.0 - - - +
532C ALA* 1.3 60.9 + - - +
534C GLN* 3.0 24.6 + - - +
535C LEU* 3.2 28.3 + - + +
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Residues in contact with ALA 532 (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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395C GLY* 6.1 0.2 - - - -
438C PHE* 3.6 31.0 - - + -
440C LEU* 3.9 16.5 - - + +
443C CYS* 4.6 1.8 - - - -
447C MET* 4.1 2.4 - - - +
499C CYS* 3.7 28.1 - - + -
529C LEU* 3.6 12.4 + - + +
530C HIS 3.1 0.6 - - - -
531C ARG* 1.3 78.6 - - - +
533C LEU* 1.3 62.7 + - - +
535C LEU* 3.3 5.9 + - - +
536C LEU* 3.1 17.5 + - - +
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Residues in contact with LEU 533 (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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354B VAL* 3.3 31.4 - - + +
356B PRO* 3.4 24.0 - - + -
366B GLN* 4.1 11.0 - - + -
496C ARG* 4.2 19.5 - - + +
499C CYS* 3.1 33.2 - - + +
528C HIS* 4.0 35.0 - - + -
529C LEU 3.1 15.5 + - - +
530C HIS 2.8 9.7 + - - +
532C ALA* 1.3 80.2 - - - +
534C GLN* 1.3 61.3 + - - +
536C LEU* 3.4 2.1 + - + -
537C ASP* 3.1 16.6 + - - +
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Residues in contact with GLN 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASP* 4.1 19.5 + - - +
356B PRO* 4.7 2.7 - - + -
357B SER* 3.0 23.4 + - - +
317C HIS* 3.3 32.3 + - + +
318C PRO 4.0 3.8 + - - -
320C PRO* 3.1 30.8 - - + +
530C HIS 3.0 12.0 + - - +
531C ARG* 3.0 31.9 + - - +
532C ALA 3.2 0.2 - - - -
533C LEU* 1.3 73.9 - - - +
535C LEU* 1.3 60.4 + - + +
537C ASP* 2.7 34.4 + - - +
538C GLU* 3.0 11.3 + - - +
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Residues in contact with LEU 535 (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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314C ILE* 4.1 22.4 - - + +
315C SER* 3.5 33.0 - - - +
440C LEU* 3.4 45.5 - - + -
444C HIS* 4.2 13.4 + - + +
447C MET* 3.6 15.7 - - + -
531C ARG* 3.2 18.5 + - + +
532C ALA 3.3 4.0 + - - +
534C GLN* 1.3 80.3 - - + +
536C LEU* 1.3 56.5 + - - +
538C GLU* 3.4 13.6 + - - +
539C VAL* 3.0 30.8 + - - +
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Residues in contact with LEU 536 (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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354B VAL* 3.7 19.1 - - + -
447C MET* 3.5 28.4 - - + -
492C VAL 4.9 0.4 - - - +
495C LEU* 3.6 33.4 - - + +
496C ARG* 3.3 40.4 - - + +
499C CYS* 4.2 6.7 - - - -
532C ALA 3.1 9.6 + - - +
533C LEU* 3.7 8.3 - - + +
534C GLN 3.1 0.8 - - - -
535C LEU* 1.3 74.7 - - - +
537C ASP* 1.3 61.4 + - - +
539C VAL* 3.4 10.0 + - + -
540C LEU* 2.9 43.3 + - + +
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Residues in contact with ASP 537 (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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353B TYR* 3.3 28.6 - - - +
354B VAL* 3.5 6.7 + - - +
355B ASP* 3.0 25.7 - - + +
361B ARG* 2.5 32.7 + - - -
533C LEU 3.1 12.2 + - - +
534C GLN* 2.7 20.5 + - - +
536C LEU* 1.3 71.2 - - - +
538C GLU* 1.3 62.7 + - + +
540C LEU* 3.0 5.5 + - - +
541C HIS* 3.0 38.2 + - - -
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Residues in contact with GLU 538 (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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315C SER* 3.2 26.6 + - - -
317C HIS* 3.6 26.7 - - + +
534C GLN* 3.0 11.4 + - - +
535C LEU* 3.7 16.7 - - + +
537C ASP* 1.3 74.2 - - + +
539C VAL* 1.3 65.9 + - + +
541C HIS* 2.9 19.5 + - - +
542C THR* 3.0 21.2 + - + +
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Residues in contact with VAL 539 (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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444C HIS* 4.2 8.3 - - + -
447C MET* 4.0 16.2 - - + -
448C GLN* 3.9 35.9 - - + +
451C ALA* 3.9 26.9 - - + -
535C LEU 3.0 19.8 + - - +
536C LEU* 3.5 18.4 - - + +
538C GLU* 1.3 76.1 - - + +
540C LEU* 1.3 62.9 + - - +
542C THR* 2.6 28.4 + - - +
543C MET* 3.4 10.0 - - + +
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 4.0 33.1 + - + -
354B VAL* 3.9 31.9 - - + +
451C ALA* 5.3 1.8 - - + -
490C ILE* 5.6 0.9 - - + +
492C VAL* 4.0 29.6 - - + -
495C LEU* 4.0 22.4 - - + -
536C LEU* 2.9 29.1 + - + +
537C ASP* 3.3 7.6 - - - +
539C VAL* 1.3 73.8 - - + +
541C HIS* 1.3 59.4 + - - +
542C THR 3.1 9.4 + - - -
543C MET* 3.3 27.8 + - + +
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Residues in contact with HIS 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP* 5.5 0.2 - - - -
353B TYR* 3.3 31.8 + + - -
361B ARG* 3.3 28.6 + - - -
385B LYS* 5.0 13.0 + - + -
537C ASP* 3.0 38.4 + - + -
538C GLU* 2.9 15.4 + - + +
540C LEU* 1.3 74.8 - - - +
542C THR* 1.3 59.3 + - + +
543C MET 3.4 3.9 - - - +
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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