Contacts of the helix formed by residues 485 - 500 (chain R) in PDB entry 1G4W
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 VAL 485 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315R ILE* 4.3 20.2 - - + -
483R GLY* 2.9 16.9 + - - -
484R GLY* 1.3 84.2 - - - +
486R GLY* 1.3 76.0 + - - +
488R THR* 4.0 1.4 - - - -
489R GLY* 3.2 10.7 + - - -
516R ARG* 4.1 1.8 - - - +
517R ASN* 3.3 36.3 - - - +
519R ARG* 3.7 24.2 - - + +
520R MET* 3.5 7.6 - - - -
521R LEU 3.0 20.7 + - - -
522R GLU* 4.0 19.5 - - - +
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Residues in contact with GLY 486 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481R CYS* 4.5 0.8 - - - -
483R GLY 4.3 3.0 + - - -
485R VAL* 1.3 82.8 - - - +
487R ARG* 1.3 66.5 + - - +
488R THR 3.1 1.1 - - - +
489R GLY 2.9 12.0 + - - -
490R THR* 3.2 9.9 + - - -
521R LEU* 4.5 6.3 + - - -
522R GLU* 5.0 15.3 - - - -
523R ASP* 6.2 0.7 - - - -
526R GLN* 3.4 15.1 - - - +
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Residues in contact with ARG 487 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375R LEU* 3.4 33.8 + - + +
376R THR* 4.2 2.8 - - - +
377R SER* 4.6 1.6 - - - +
380R GLN* 2.9 27.5 + - - +
439R TRP* 2.8 76.3 + - + +
440R PRO 3.9 5.2 - - - -
441R ASP* 3.3 38.5 + - - +
442R HIS 4.9 0.9 - - - +
481R CYS* 3.8 27.4 - - + +
482R LEU* 4.1 6.5 - - - +
486R GLY* 1.3 71.1 - - - +
488R THR* 1.3 63.6 + - - +
490R THR* 3.1 3.1 + - - -
491R MET* 2.9 24.8 + - - +
526R GLN* 3.5 18.5 + - - +
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Residues in contact with THR 488 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336R LEU* 5.2 1.3 - - + -
346R ALA* 3.5 32.1 - - + -
375R LEU* 3.6 8.7 - - - +
479R ILE* 3.7 21.5 - - + +
480R HIS* 3.4 6.1 - - - -
481R CYS* 3.0 37.4 + - - -
483R GLY 3.8 1.4 + - - -
484R GLY* 3.9 17.3 - - - +
486R GLY 3.1 0.4 - - - -
487R ARG* 1.3 78.7 - - - +
489R GLY* 1.3 63.3 + - - +
491R MET* 3.4 2.3 + - - +
492R ALA* 3.1 23.1 + - + +
520R MET* 4.5 2.2 - - + -
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Residues in contact with GLY 489 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485R VAL 3.2 13.6 + - - -
486R GLY 2.9 8.7 + - - -
488R THR* 1.3 80.9 - - - +
490R THR* 1.3 55.3 + - - +
492R ALA* 4.6 0.2 - - - -
493R ALA* 2.9 25.6 + - - +
512R PHE* 3.3 14.2 - - - -
520R MET* 3.5 17.5 - - - +
521R LEU* 3.8 13.9 - - - -
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Residues in contact with THR 490 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439R TRP* 3.9 19.3 - - + -
451R LEU* 4.2 13.9 - - + -
486R GLY 3.2 3.0 + - - -
487R ARG 3.1 7.5 + - - -
489R GLY* 1.3 73.2 - - - +
491R MET* 1.3 55.9 + - - +
493R ALA* 3.0 5.4 + - - +
494R ALA* 2.7 34.2 + - - +
521R LEU* 3.6 14.9 - - - +
526R GLN* 2.7 41.6 + - + +
529R GLN* 5.3 1.8 - - - +
530R LEU* 3.8 22.4 - - + +
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Residues in contact with MET 491 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373R VAL* 3.5 28.3 - - + -
375R LEU* 3.7 17.0 - - + -
439R TRP* 3.4 26.7 - - + -
451R LEU* 5.1 3.4 - - - -
454R LEU* 4.0 31.6 - - - -
455R ALA* 5.0 3.6 - - - -
458R VAL* 3.5 22.7 - - + -
479R ILE* 3.9 20.0 - - + -
487R ARG 2.9 12.4 + - - +
488R THR 3.6 4.7 - - - +
490R THR* 1.3 74.8 - - - +
492R ALA* 1.3 62.9 + - - +
494R ALA* 3.2 10.1 + - - +
495R LEU* 3.1 26.9 + - + +
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Residues in contact with ALA 492 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336R LEU* 3.6 16.6 - - + -
343R VAL* 4.0 9.4 - - + +
344R ALA* 4.7 2.0 - - + -
479R ILE* 4.0 15.6 - - + +
488R THR 3.1 14.4 + - - +
491R MET* 1.3 79.0 - - - +
493R ALA* 1.3 64.0 - - - +
495R LEU* 3.0 19.0 + - - +
496R VAL* 3.2 14.4 + - - +
512R PHE* 3.6 24.2 - - + -
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Residues in contact with ALA 493 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489R GLY 2.9 15.1 + - - +
490R THR 3.3 7.9 - - - +
492R ALA* 1.3 75.8 - - - +
494R ALA* 1.3 57.5 + - - +
496R VAL* 2.9 20.6 + - - +
497R LEU* 3.1 15.2 + - - +
505R LEU* 4.9 6.1 - - + +
508R VAL* 4.0 21.1 - - + -
512R PHE* 3.5 9.3 - - + -
521R LEU* 4.5 4.0 - - + -
530R LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 494 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451R LEU* 4.1 17.9 - - + -
455R ALA* 4.2 11.4 - - + -
490R THR 2.7 15.9 + - - +
491R MET* 3.3 12.6 - - - +
492R ALA 3.1 0.2 - - - -
493R ALA* 1.3 73.7 - - - +
495R LEU* 1.3 60.6 + - - +
497R LEU* 3.5 1.9 + - - +
498R LYS* 3.3 13.2 + - - +
530R LEU* 3.9 7.4 - - + +
533R MET* 3.1 43.8 - - + +
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Residues in contact with LEU 495 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343R VAL* 4.9 11.2 - - + +
344R ALA* 5.2 0.2 - - + -
455R ALA* 3.7 29.2 - - - +
458R VAL* 3.8 21.8 - - + -
459R LYS* 4.4 19.5 - - + +
477R PRO* 3.9 27.6 - - + -
479R ILE* 4.0 17.7 - - + -
491R MET* 3.1 19.7 + - + +
492R ALA* 3.0 10.8 + - - +
494R ALA* 1.3 75.3 - - - +
496R VAL* 1.3 64.8 + - - +
498R LYS* 3.5 6.1 + - + +
499R ASP* 3.1 22.5 + - - +
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Residues in contact with VAL 496 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338R PHE* 3.7 21.3 - - + -
343R VAL* 3.9 31.6 - - + -
492R ALA 3.2 12.7 + - - +
493R ALA* 2.9 10.4 + - - +
495R LEU* 1.3 77.5 - - - +
497R LEU* 1.3 60.7 + - + +
499R ASP* 3.2 6.6 + - - +
500R ASN* 2.8 27.9 + - - +
503R SER* 3.3 28.7 + - - +
508R VAL* 4.0 9.9 - - + -
512R PHE* 4.3 11.4 - - + -
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Residues in contact with LEU 497 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493R ALA 3.1 9.8 + - - +
494R ALA 3.8 5.6 - - - +
495R LEU 3.4 0.2 - - - -
496R VAL* 1.3 80.3 - - + +
498R LYS* 1.3 58.2 + - - +
500R ASN 3.6 4.9 - - - +
501R PRO* 2.8 42.8 - - + +
503R SER* 4.3 6.1 - - - +
505R LEU* 3.8 27.6 - - + -
530R LEU* 3.9 21.3 - - + +
533R MET* 4.1 10.8 - - + -
534R GLN* 3.4 57.2 - - + +
537R LEU* 3.6 14.3 - - + +
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Residues in contact with LYS 498 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452R GLU* 3.1 47.6 + - - +
455R ALA* 3.8 16.4 - - + +
456R ASP* 3.0 31.3 + - - +
459R LYS* 5.6 11.7 - - + -
494R ALA 3.3 15.2 + - - +
495R LEU* 3.8 8.1 - - + +
496R VAL 3.2 0.4 - - - -
497R LEU* 1.3 75.8 - - - +
499R ASP* 1.3 66.9 + - - +
500R ASN 3.4 0.2 + - - -
501R PRO* 4.4 4.3 - - - +
533R MET* 4.0 5.2 - - + -
537R LEU* 3.9 18.4 - - + +
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Residues in contact with ASP 499 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459R LYS* 5.9 6.7 - - - +
495R LEU 3.1 17.0 + - - +
496R VAL* 3.2 6.5 + - - +
498R LYS* 1.3 78.1 - - - +
500R ASN* 1.3 69.7 + - - +
501R PRO* 4.3 2.0 - - - +
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Residues in contact with ASN 500 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496R VAL 2.8 10.7 + - - +
497R LEU* 3.1 4.3 - - - +
498R LYS 3.2 0.4 - - - -
499R ASP* 1.3 88.9 - - - +
501R PRO* 1.3 67.6 - - - +
502R HIS* 3.0 36.4 + - - +
503R SER* 2.9 31.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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