Contacts of the helix formed by residues 398 - 413 (chain S) in PDB entry 5GJQ
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 LEU 398 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334S VAL* 5.9 0.4 - - + -
337S LEU* 3.4 33.0 - - + -
338S LEU* 3.5 33.2 - - + +
363S LEU* 5.1 1.8 - - + -
367S VAL* 4.7 3.4 - - + -
375S PHE* 3.9 17.5 - - + -
395S ILE* 2.9 38.9 + - + +
397S ARG* 1.3 76.7 - - - +
399S ARG* 1.3 53.2 - - - +
400S HIS* 2.9 0.9 - - - -
401S ASN* 2.5 56.1 + - + +
402S VAL* 2.8 20.0 + - + -
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Residues in contact with ARG 399 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372S LEU* 3.3 44.1 - - + +
375S PHE* 3.7 24.2 - - + -
376S ASN* 3.5 18.4 - - - -
396S ILE* 4.0 16.1 + - - +
397S ARG 2.9 1.5 + - - +
398S LEU* 1.3 77.0 - - - +
400S HIS* 1.3 60.5 + - - +
402S VAL* 4.2 5.1 - - - +
403S ILE* 3.2 38.3 + - + +
234T GLN* 4.5 27.8 - - + +
235T TYR* 6.1 2.6 - - - -
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Residues in contact with HIS 400 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397S ARG* 3.2 19.3 + - + +
398S LEU 2.7 3.8 + - - -
399S ARG* 1.3 73.8 - - - +
401S ASN* 1.3 92.7 + - - -
403S ILE* 3.1 7.4 + - - +
404S LYS* 2.9 44.4 + - - +
237T MET* 5.2 20.9 - - + +
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Residues in contact with ASN 401 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337S LEU 3.6 5.6 + - - +
338S LEU* 2.6 46.6 + - - +
340S GLY* 5.2 5.2 - - - -
367S VAL* 5.3 6.7 - - + -
397S ARG 5.9 0.2 - - - -
398S LEU* 2.5 28.5 + - + +
400S HIS* 1.3 89.9 - - - +
402S VAL* 1.3 63.6 + - - +
404S LYS* 3.0 24.4 + - - +
405S THR* 2.9 25.9 + - - +
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Residues in contact with VAL 402 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366S ALA 4.6 2.5 - - - +
367S VAL* 3.7 34.3 - - + -
370S GLY* 3.8 26.7 - - - +
371S ASN 4.4 2.0 - - - +
372S LEU* 4.2 22.7 - - + +
375S PHE* 4.0 26.5 - - + -
398S LEU 2.8 21.7 + - - +
399S ARG* 4.2 5.6 - - - +
401S ASN* 1.3 70.7 - - - +
403S ILE* 1.3 66.6 + - + +
405S THR* 3.0 11.9 + - - -
406S GLY 2.9 22.3 + - - -
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Residues in contact with ILE 403 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370S GLY 5.5 1.6 - - - +
372S LEU* 4.1 29.8 - - + -
399S ARG* 3.2 25.4 - - + +
400S HIS* 3.1 7.4 + - - +
402S VAL* 1.3 82.2 - - + +
404S LYS* 1.3 68.2 + - - +
406S GLY* 3.0 3.8 + - - +
407S VAL* 2.9 34.0 + - + +
426S LEU* 4.8 15.3 - - + -
428S LEU* 5.5 13.2 - - + -
437S ILE* 5.5 11.4 - - + -
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Residues in contact with LYS 404 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400S HIS* 2.9 35.2 + - - +
401S ASN* 3.2 30.1 + - - +
403S ILE* 1.3 77.0 - - - +
405S THR* 1.3 64.2 + - - +
407S VAL* 3.1 7.3 + - - +
408S ARG* 2.9 29.7 + - - +
441S ALA* 6.2 5.4 - - + -
444S ASP* 4.9 12.1 + - - -
446S VAL* 4.9 18.4 - - + +
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Residues in contact with THR 405 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367S VAL* 3.6 23.9 + - - +
368S ARG* 3.4 28.0 - - - +
369S THR 4.8 0.4 - - - -
370S GLY* 4.4 2.5 - - - +
401S ASN* 2.9 14.1 + - - +
402S VAL 3.2 9.0 - - - -
404S LYS* 1.3 75.8 - - - +
406S GLY* 1.3 65.3 - - - +
408S ARG* 3.0 27.9 + - - +
409S MET* 2.9 34.1 + - + +
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Residues in contact with GLY 406 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369S THR 5.1 2.2 - - - -
370S GLY* 4.1 19.5 - - - -
402S VAL 2.9 13.5 + - - -
403S ILE* 3.0 4.6 + - - -
405S THR* 1.3 76.8 - - - +
407S VAL* 1.3 55.9 + - - +
409S MET* 3.4 4.3 + - - +
410S ILE* 3.0 38.7 + - - +
426S LEU* 4.2 11.4 - - - -
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Residues in contact with VAL 407 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403S ILE* 2.9 32.4 + - + +
404S LYS* 3.5 8.1 - - - +
406S GLY* 1.3 72.0 - - - +
408S ARG* 1.3 61.5 + - - +
410S ILE* 3.3 8.9 + - - +
411S SER* 2.8 28.9 + - - -
422S ILE* 5.9 1.1 - - + -
426S LEU* 4.4 11.4 - - + -
437S ILE* 5.5 7.0 - - + +
438S VAL* 5.0 17.7 - - + -
441S ALA* 4.8 13.2 - - + -
446S VAL* 5.6 0.9 - - + -
447S ILE* 3.7 12.9 - - + +
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Residues in contact with ARG 408 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340S GLY* 4.9 12.5 + - - -
404S LYS* 2.9 19.5 + - - +
405S THR* 3.7 31.6 + - - +
407S VAL* 1.3 76.6 - - - +
409S MET* 1.3 59.9 + - + +
411S SER* 2.3 27.7 + - - +
412S LEU* 2.9 29.6 + - + +
446S VAL* 4.0 28.9 - - + +
447S ILE* 3.9 5.2 - - - -
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Residues in contact with MET 409 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335R SER 6.0 1.8 - - - +
339R ALA* 4.7 19.4 - - + +
368S ARG 4.9 5.4 - - - +
369S THR 5.7 4.0 - - - +
405S THR* 2.9 30.9 + - + +
406S GLY* 3.9 4.3 - - - +
408S ARG* 1.3 75.7 - - + +
410S ILE* 1.3 66.2 + - + +
411S SER 3.0 2.0 + - - -
412S LEU* 3.2 6.2 + - + +
413S SER* 2.8 27.3 + - - -
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Residues in contact with ILE 410 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406S GLY* 3.0 23.2 + - - +
407S VAL* 3.7 6.3 - - - +
409S MET* 1.3 75.0 - - + +
411S SER* 1.3 60.7 + - - +
413S SER* 3.8 5.8 - - - -
414S TYR* 3.2 33.5 + - + +
417S ILE* 4.7 7.5 - - + +
422S ILE* 4.0 31.9 - - + -
425S LYS* 4.2 25.6 - - + -
426S LEU* 3.7 39.3 - - + -
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Residues in contact with SER 411 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407S VAL 2.8 12.9 + - - -
408S ARG* 2.3 34.0 + - - +
410S ILE* 1.3 75.2 - - - +
412S LEU* 1.3 69.9 + - - +
413S SER 3.1 1.8 - - - -
414S TYR 2.7 25.6 - - - +
446S VAL 5.4 0.2 + - - -
447S ILE* 3.6 34.5 + - - +
460S SER* 4.5 9.6 + - - -
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Residues in contact with LEU 412 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338R ILE* 3.4 14.8 - - + +
339R ALA* 4.4 35.4 - - + +
346R LYS* 4.0 12.6 - - - +
408S ARG* 2.9 30.2 + - + +
409S MET* 3.2 4.0 + - + +
411S SER* 1.3 86.1 + - - +
413S SER* 1.3 58.9 + - - +
414S TYR 3.6 0.3 + - - -
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Residues in contact with SER 413 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335R SER* 4.2 28.6 - - - -
338R ILE* 3.8 18.2 - - - -
339R ALA* 5.3 2.5 - - - -
347R ILE* 3.0 27.2 - - - +
409S MET 2.8 21.9 + - - -
410S ILE* 3.8 0.2 - - - -
412S LEU* 1.3 77.2 - - - +
414S TYR* 1.3 87.8 + - - +
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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