Contacts of the helix formed by residues 530 - 541 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A PRO* 3.4 40.8 - - + +
357A SER* 5.2 1.8 + - - -
320B PRO* 4.1 9.9 - - + +
322B TYR* 3.4 43.7 + + + +
323B TRP 3.0 7.3 + - - +
324B CYS* 3.7 8.5 - - - -
325B SER* 3.0 34.7 + - - -
340B LYS* 5.4 2.5 - - + -
528B HIS* 3.1 18.3 - - + +
529B LEU* 1.3 69.6 - - - +
531B ARG* 1.3 55.4 + - - +
532B ALA 3.0 1.8 - - - -
533B LEU* 2.9 4.1 + - + +
534B GLN* 2.7 39.3 + - + +
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Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER* 3.1 36.7 + - - -
317B HIS* 3.0 28.6 + - - +
318B PRO 3.5 11.1 + - - -
319B ALA* 3.8 4.6 - - - +
320B PRO* 4.3 16.5 - - + +
323B TRP* 4.2 6.3 + - + +
394B GLU* 2.8 52.5 + - - +
395B GLY* 4.8 6.5 - - - -
440B LEU* 4.1 16.2 - - + -
529B LEU* 3.6 0.6 - - - +
530B HIS* 1.3 78.3 - - - +
532B ALA* 1.3 60.5 + - - +
534B GLN* 3.0 28.7 + - - +
535B LEU* 3.1 26.2 + - - +
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 3.7 31.6 - - + -
440B LEU* 4.3 11.1 - - + +
443B CYS* 4.7 3.6 - - - -
447B MET* 4.1 2.4 - - - +
499B CYS* 3.7 26.0 - - + -
529B LEU* 3.7 10.3 + - + +
530B HIS 3.0 0.6 - - - -
531B ARG* 1.3 78.1 - - - +
533B LEU* 1.3 60.5 + - - +
535B LEU* 3.1 6.6 + - - +
536B LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.3 22.2 - - + +
355A ASP* 4.0 0.3 - - - -
356A PRO* 3.3 35.9 - - + -
366A GLN* 4.1 15.5 - - + -
496B ARG* 4.5 6.1 - - - +
499B CYS* 3.2 28.5 - - + +
500B ILE* 5.2 2.0 - - + -
528B HIS* 4.0 27.8 - - + -
529B LEU 2.9 24.9 - - - +
530B HIS 2.9 3.1 + - - +
532B ALA* 1.3 74.7 - - - +
534B GLN* 1.3 66.2 + - - +
536B LEU* 4.0 7.4 - - + -
537B ASP* 3.2 22.2 + - - +
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Residues in contact with GLN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASP* 4.0 19.4 + - - +
356A PRO* 5.1 2.5 - - + -
357A SER* 3.8 19.1 + - - +
317B HIS* 3.6 33.8 + - + +
318B PRO 3.4 10.4 + - - +
320B PRO* 3.6 20.8 - - + +
530B HIS* 2.7 25.9 + - + +
531B ARG* 3.0 42.8 + - - +
532B ALA 3.2 0.2 - - - -
533B LEU* 1.3 75.2 - - - +
535B LEU* 1.3 65.4 + - + +
537B ASP* 3.4 3.1 - - - +
538B GLU* 2.9 23.3 + - - +
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 3.7 17.9 - - + -
315B SER* 3.6 31.4 - - - +
317B HIS* 5.7 1.1 - - + -
394B GLU* 4.4 0.4 - - - +
440B LEU* 3.2 35.2 - - + -
444B HIS* 3.7 29.8 - - + +
447B MET* 4.3 5.4 - - + -
531B ARG* 3.1 24.9 - - - +
532B ALA 3.3 5.2 - - - +
534B GLN* 1.3 80.0 - - + +
536B LEU* 1.3 51.9 + - - +
538B GLU* 2.8 15.9 + - - +
539B VAL* 2.7 38.0 + - - +
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.4 22.0 - - + -
447B MET* 3.5 25.4 - - + -
492B VAL* 5.3 0.7 - - + +
495B LEU* 3.5 61.9 - - + +
496B ARG* 3.6 11.9 - - + +
499B CYS* 3.9 8.5 - - - -
532B ALA 3.0 10.4 + - - +
533B LEU* 4.0 6.3 - - + +
535B LEU* 1.3 77.4 - - - +
537B ASP* 1.3 52.7 + - - +
539B VAL* 2.9 12.1 + - + +
540B LEU* 2.8 42.0 + - + +
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Residues in contact with ASP 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.0 17.5 - - - +
354A VAL* 3.6 9.9 + - + -
355A ASP* 3.7 19.1 + - + +
361A ARG* 2.8 44.9 + - - -
533B LEU 3.2 16.7 + - - +
534B GLN 3.4 4.3 - - - +
536B LEU* 1.3 77.6 - - - +
538B GLU* 1.3 67.1 + - - +
540B LEU* 2.9 19.2 + - - +
541B HIS* 3.0 22.5 + - - +
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Residues in contact with GLU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ILE 5.3 0.5 - - - +
315B SER* 3.3 27.8 + - - -
317B HIS* 3.2 29.3 - - + +
444B HIS* 5.8 3.3 - - - -
534B GLN 2.9 13.1 + - - +
535B LEU* 2.8 20.4 + - - +
537B ASP* 1.3 77.1 + - - +
539B VAL* 1.3 57.4 + - + +
541B HIS* 3.5 10.3 + - - +
542B THR* 3.0 29.5 + - + +
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B HIS* 4.1 23.8 - - + +
447B MET* 4.8 6.3 - - + +
448B GLN* 4.5 21.3 - - + +
451B ALA* 4.1 25.8 - - + -
535B LEU 2.7 25.4 + - - +
536B LEU* 2.9 19.5 + - + +
538B GLU* 1.3 72.0 - - + +
540B LEU* 1.3 60.1 + - + +
541B HIS 3.0 1.8 - - - -
542B THR* 2.6 34.6 + - - +
543B MET* 3.6 7.2 - - + +
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A TYR* 3.9 33.5 + - + -
354A VAL* 3.9 28.5 - - + -
451B ALA* 5.4 0.9 - - + -
489B GLY* 6.1 0.2 - - - -
490B ILE 5.3 1.6 - - - +
492B VAL* 4.2 31.9 - - + -
495B LEU* 4.0 26.5 - - + -
536B LEU* 2.8 23.1 + - + +
537B ASP* 2.9 6.3 + - - +
539B VAL* 1.3 75.3 - - + +
541B HIS* 1.3 61.3 + - - +
542B THR 3.2 1.3 + - - -
543B MET* 3.6 28.6 + - - +
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Residues in contact with HIS 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A TYR* 3.4 48.4 - + - -
361A ARG* 3.4 25.5 + - - -
385A LYS* 5.6 3.7 - - - -
537B ASP* 3.0 23.8 + - - +
538B GLU* 3.9 8.4 - - - +
539B VAL 3.0 1.0 - - - -
540B LEU* 1.3 77.1 - - - +
542B THR* 1.3 59.0 + - + +
543B MET 3.4 6.1 + - - +
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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