Contacts of the helix formed by residues 530 - 540 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A PRO* 3.9 8.6 - - + +
321A GLU 5.6 0.2 + - - -
322A TYR* 3.0 54.6 + + + +
323A TRP 3.0 8.1 + - - +
324A CYS* 4.0 3.1 - - - -
325A SER* 3.3 27.8 + - - -
340A LYS* 5.7 1.8 - - + -
528A HIS* 3.5 19.0 - - + +
529A LEU* 1.3 69.9 - - - +
531A ARG* 1.3 65.8 + - - +
533A LEU* 3.3 2.2 + - + +
534A GLN* 3.0 28.0 + - + +
356C PRO* 3.4 43.9 - - + +
357C SER* 5.7 1.4 - - - -
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Residues in contact with ARG 531 (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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313A PRO* 5.3 0.2 - - - +
315A SER* 3.1 34.8 + - - -
317A HIS* 3.1 17.2 + - - +
318A PRO 2.8 30.5 + - - -
319A ALA* 4.1 3.8 - - - +
320A PRO* 3.8 17.9 - - + +
323A TRP* 4.2 7.2 + - + +
394A GLU* 2.6 60.7 + - + +
395A GLY* 4.4 9.0 - - - -
440A LEU* 4.2 12.1 - - + -
529A LEU* 3.5 0.8 - - - +
530A HIS* 1.3 77.4 - - - +
532A ALA* 1.3 64.4 + - - +
534A GLN* 2.8 22.5 + - - +
535A LEU* 3.3 18.5 + - + +
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Residues in contact with ALA 532 (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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395A GLY 5.9 0.2 + - - -
438A PHE* 3.6 32.1 - - + -
440A LEU* 3.9 15.2 - - + +
443A CYS* 4.3 3.6 - - - -
447A MET* 3.9 2.3 - - - +
499A CYS* 3.7 26.4 - - + -
529A LEU* 3.7 9.7 + - + +
530A HIS 3.3 0.4 - - - -
531A ARG* 1.3 76.1 - - - +
533A LEU* 1.3 66.9 + - - +
535A LEU* 3.2 9.6 + - - +
536A LEU* 3.1 15.8 + - - +
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Residues in contact with LEU 533 (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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496A ARG* 4.6 6.5 - - + +
499A CYS* 3.9 23.8 - - + +
500A ILE* 5.7 0.7 - - + -
528A HIS* 4.0 20.6 - - + -
529A LEU 3.1 26.2 + - - +
530A HIS* 3.6 5.4 - - + +
531A ARG 3.2 0.4 - - - -
532A ALA* 1.3 73.9 - - - +
534A GLN* 1.3 65.3 + - - +
536A LEU* 3.1 8.5 + - + +
537A ASP* 3.0 18.5 + - - +
354C VAL* 3.5 41.9 - - + +
356C PRO* 3.6 19.5 - - + -
366C GLN* 3.9 28.0 - - + -
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Residues in contact with GLN 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A HIS* 3.2 39.4 + - + +
318A PRO* 3.1 7.4 + - - +
319A ALA 4.9 0.4 - - - -
320A PRO* 3.4 24.6 - - + +
530A HIS 3.0 15.0 + - - +
531A ARG* 2.8 37.1 + - - +
532A ALA 3.2 0.2 - - - -
533A LEU* 1.3 76.5 - - - +
535A LEU* 1.3 58.6 + - + +
537A ASP* 2.8 29.3 + - - +
538A GLU* 2.8 14.2 + - - +
355C ASP* 3.9 15.2 + - - +
356C PRO* 4.7 2.0 - - + -
357C SER* 3.2 21.0 + - - +
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 4.2 11.9 - - + -
315A SER* 3.5 32.3 - - - +
317A HIS* 5.7 1.1 - - + -
394A GLU* 4.7 0.9 - - - +
440A LEU* 3.7 32.5 - - + -
444A HIS* 3.6 37.4 - - + +
447A MET* 3.9 6.3 - - + -
531A ARG* 3.6 22.4 - - - +
532A ALA* 3.2 8.0 + - - +
534A GLN* 1.3 79.8 - - + +
536A LEU* 1.3 57.7 + - - +
538A GLU* 3.4 15.2 + - - +
539A VAL* 3.0 33.6 + - - +
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Residues in contact with LEU 536 (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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447A MET* 3.7 26.6 - - + +
492A VAL 5.0 1.1 - - - +
495A LEU* 3.8 27.8 - - + +
496A ARG* 3.6 36.6 - - + +
499A CYS* 4.2 7.9 - - - -
532A ALA 3.1 11.7 + - - +
533A LEU* 3.3 12.3 - - + +
534A GLN 3.0 1.0 - - - -
535A LEU* 1.3 74.5 - - - +
537A ASP* 1.3 59.6 + - - +
539A VAL* 3.0 9.6 + - + +
540A LEU* 2.9 47.7 + - + +
354C VAL* 3.6 21.3 - - + -
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Residues in contact with ASP 537 (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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317A HIS* 5.9 3.0 - - + -
533A LEU 3.0 10.6 + - - +
534A GLN* 2.8 12.8 + - - +
536A LEU* 1.3 72.0 - - - +
538A GLU* 1.3 63.7 + - - +
539A VAL 3.1 0.9 + - - -
540A LEU* 3.1 15.2 + - - +
541A HIS* 3.4 27.7 + - - -
353C TYR* 2.9 34.0 - - - +
354C VAL* 3.1 9.9 + - + +
355C ASP* 3.7 22.9 - - + +
361C ARG* 2.5 33.5 + - - -
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Residues in contact with GLU 538 (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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314A ILE* 5.4 0.7 - - - +
315A SER* 2.9 33.7 + - - -
317A HIS* 3.9 20.1 + - + +
444A HIS* 4.8 10.4 - - - -
534A GLN 2.8 10.9 + - - +
535A LEU* 3.5 16.7 - - - +
537A ASP* 1.3 77.4 + - - +
539A VAL* 1.3 62.1 + - + +
541A HIS* 3.8 9.7 + - - +
542A THR* 3.4 22.1 - - + +
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A HIS* 4.4 10.5 - - + -
447A MET* 4.3 11.0 - - - +
448A GLN* 4.2 24.7 - - + +
451A ALA* 4.4 20.0 - - + -
535A LEU 3.0 22.6 + - - +
536A LEU* 3.0 17.0 + - + +
538A GLU* 1.3 79.1 - - + +
540A LEU* 1.3 57.6 + - + +
541A HIS 3.0 5.2 - - - -
542A THR* 2.9 19.6 + - - +
543A MET* 3.1 33.3 + - + +
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Residues in contact with LEU 540 (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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451A ALA* 5.2 1.1 - - + -
492A VAL* 4.5 24.2 - - + -
495A LEU* 4.0 26.7 - - + -
536A LEU* 2.9 35.2 + - + +
537A ASP* 3.1 3.3 + - - +
539A VAL* 1.3 79.0 - - + +
541A HIS* 1.3 63.5 + - - +
542A THR 3.4 1.6 - - - -
543A MET 4.4 6.7 - - - +
544A PRO* 3.8 18.8 - - - +
545A ILE* 4.1 21.9 + - + +
353C TYR* 3.7 32.1 + - + -
354C VAL* 4.3 13.7 - - + +
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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