Contacts of the helix formed by residues 395 - 405 (chain A) in PDB entry 2Q8J
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 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LEU* 1.3 75.5 - - - +
396A GLY* 1.3 69.9 + - - +
397A GLY* 2.8 14.8 + - - -
398A TYR* 2.9 20.1 + - + -
399A ILE* 3.1 10.8 + - - +
433A TYR* 2.9 8.3 + - - -
463A ARG* 3.1 20.7 - - + +
464A THR* 2.8 25.3 + - - -
595A HIS* 2.9 22.8 + - + +
801A FE 2.2 30.8 - - - -
802A CO3 3.0 9.1 + - - +
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Residues in contact with GLY 396 (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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394A LEU 4.2 0.2 + - - -
395A ASP* 1.3 78.5 + - - +
397A GLY* 1.3 62.6 + - - +
399A ILE* 3.2 13.3 + - - +
400A TYR* 3.4 8.7 + - - +
464A THR* 3.7 8.4 + - - -
593A PRO* 4.5 12.8 + - - -
594A ASN 4.8 1.4 + - - -
595A HIS* 4.2 4.4 - - - -
661A LEU* 3.4 28.3 - - - +
665A TYR* 3.7 10.0 - - - -
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Residues in contact with GLY 397 (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 ASP* 2.8 13.6 + - - -
396A GLY* 1.3 72.8 - - - +
398A TYR* 1.3 61.3 + - - +
400A TYR* 3.4 17.9 + - - +
401A THR* 3.6 6.4 + - - -
462A ASP* 3.1 25.3 - - - +
464A THR* 3.3 0.4 + - - -
468A ASN* 3.6 7.3 + - - -
665A TYR* 3.2 20.6 + - - -
669A ILE* 5.6 0.3 - - - +
673A LYS* 5.6 1.4 + - - -
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Residues in contact with TYR 398 (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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377A THR* 3.1 44.5 + - + -
378A ASP* 4.6 14.4 - - - -
381A ILE* 4.0 4.3 - - + +
394A LEU* 3.8 22.7 - - + -
395A ASP* 2.9 16.9 + - + +
397A GLY* 1.3 76.6 - - - +
399A ILE* 1.4 57.8 + - - +
400A TYR 3.1 0.2 - - - -
401A THR* 2.9 10.7 + - - +
402A ALA* 2.8 28.9 + - - +
460A ALA* 4.2 6.4 - - - +
461A VAL 3.8 9.0 + - - -
462A ASP* 3.7 31.3 + - + -
463A ARG* 3.8 33.0 - - + -
517A PRO* 4.5 10.9 - - - +
524A TYR* 4.5 7.0 + - - -
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Residues in contact with ILE 399 (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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394A LEU* 4.0 21.1 - - + +
395A ASP 3.1 16.7 + - - +
396A GLY* 3.2 12.9 + - - +
398A TYR* 1.4 75.5 - - - +
400A TYR* 1.3 58.1 + - - +
402A ALA* 3.6 7.4 - - + +
403A GLY* 2.8 27.9 + - - +
409A PRO* 5.2 6.7 - - + -
594A ASN 4.7 0.7 - - - +
596A ALA* 3.8 30.1 - - + +
598A VAL* 4.1 16.8 - - + -
657A TYR* 4.1 22.0 - - + +
660A TYR* 3.9 21.8 - - + -
661A LEU* 4.1 11.4 - - + -
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Residues in contact with TYR 400 (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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396A GLY 3.4 5.4 + - - +
397A GLY 3.4 11.0 - - - +
399A ILE* 1.3 80.5 - - - +
401A THR* 1.3 66.7 + - - +
403A GLY* 3.5 3.3 + - - -
404A LYS* 3.0 60.1 + - + +
657A TYR* 4.3 14.7 - + - -
661A LEU* 3.9 18.3 - - + +
666A VAL* 4.1 24.4 - - + +
669A ILE* 3.6 35.6 + - + -
670A ALA* 4.2 15.4 - - - +
673A LYS* 3.3 35.3 - - + +
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Residues in contact with THR 401 (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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378A ASP* 4.3 11.7 + - - +
381A ILE* 4.3 8.1 - - + -
397A GLY 3.6 7.0 + - - -
398A TYR* 2.9 15.8 + - - -
400A TYR* 1.3 81.3 - - - +
402A ALA* 1.3 67.0 + - - +
403A GLY 3.0 1.4 + - - -
404A LYS* 3.3 12.7 + - - +
405A CYS* 3.5 11.8 + - - -
462A ASP* 4.8 10.0 + - - -
673A LYS* 4.8 10.4 + - - -
685A ALA* 4.8 7.9 - - + -
686A PHE* 3.5 36.3 - - + -
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Residues in contact with ALA 402 (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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381A ILE* 4.1 17.7 - - + +
394A LEU* 4.0 21.3 - - + -
398A TYR 2.8 18.6 + - - +
399A ILE* 3.7 6.5 - - - +
401A THR* 1.3 74.2 - - - +
403A GLY* 1.3 55.5 + - - +
405A CYS* 3.2 15.3 + - - +
407A LEU* 3.0 43.6 + - + +
598A VAL* 4.6 4.3 - - + -
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Residues in contact with GLY 403 (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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399A ILE* 2.8 20.2 + - - -
400A TYR 3.5 0.4 + - - -
401A THR 3.0 0.4 + - - -
402A ALA* 1.3 69.0 - - - +
404A LYS* 1.3 63.8 + - - +
405A CYS 3.0 1.8 - - - -
406A GLY* 3.2 12.0 + - - -
407A LEU 3.7 12.3 - - - +
657A TYR* 3.4 40.5 - - - -
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Residues in contact with LYS 404 (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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400A TYR* 3.0 56.5 + - + +
401A THR* 3.3 7.3 + - - +
403A GLY* 1.3 76.6 - - - +
405A CYS* 1.3 60.1 + - - +
406A GLY 3.2 3.1 + - - -
657A TYR* 3.2 22.6 + - - +
658A GLU* 5.9 0.2 + - - -
666A VAL* 6.3 0.2 - - - +
681A LEU 6.1 0.4 - - - -
682A GLU* 4.8 17.1 - - + +
683A ALA 3.8 27.7 - - - +
684A CYS* 3.7 12.8 + - - +
685A ALA 5.6 0.4 - - - +
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Residues in contact with CYS 405 (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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381A ILE* 5.1 1.8 - - + -
385A LEU* 3.4 31.9 - - + +
401A THR* 3.7 13.0 - - - +
402A ALA* 3.2 11.6 + - - +
403A GLY 3.0 0.8 - - - -
404A LYS* 1.3 78.7 - - - +
406A GLY* 1.3 58.3 + - - +
407A LEU* 3.5 2.0 - - + -
684A CYS* 2.0 52.7 - - - -
685A ALA 4.1 1.3 - - - -
686A PHE* 3.7 20.0 - - - -
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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