Contacts of the helix formed by residues 39 - 53 (chain 5) in PDB entry 1G6Q
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 39 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355 GLU 3.1 10.9 + - - +
365 MET 3.7 10.8 - - - +
375 LEU 3.3 1.2 - - - -
385 GLN* 1.3 74.4 - - - +
405 THR* 1.3 62.1 + - - +
415 VAL* 3.4 12.6 + - - +
425 ARG* 3.0 31.2 + - + +
435 THR* 3.3 11.8 + - - -
2815 TYR* 3.9 10.8 - - + +
2825 THR* 2.9 14.8 + - - -
2835 HIS* 2.9 48.1 + - + +
1906 TYR* 4.5 2.0 - - - -
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Residues in contact with THR 40 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 LEU 5.6 0.2 - - - +
385 GLN* 2.8 19.1 + - - +
395 ASP* 1.3 68.3 + - - +
415 VAL* 1.3 69.7 + - - +
445 LEU* 3.0 47.6 + - + +
1906 TYR* 4.3 16.4 - - + +
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Residues in contact with VAL 41 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 ASP* 3.2 7.9 + - - +
405 THR* 1.3 79.4 + - - +
425 ARG* 1.3 61.8 + - - +
445 LEU* 5.1 0.9 - - - -
455 SER* 2.7 32.6 + - - +
2735 PHE* 4.1 30.5 - - + -
2745 SER 5.0 6.1 - - - +
2805 PRO* 4.6 24.0 - - + +
2815 TYR 3.5 21.1 - - - +
2825 THR* 5.2 5.4 - - - -
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Residues in contact with ARG 42 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 MET* 3.2 46.9 + - - +
375 LEU* 4.2 3.4 - - - +
395 ASP* 3.0 28.4 + - - +
415 VAL* 1.3 79.7 - - - +
435 THR* 1.3 94.0 + - - +
455 SER* 3.5 2.7 - - - -
465 TYR* 3.1 30.4 + - + -
715 ILE* 4.4 18.6 - - - +
725 LEU* 4.9 8.5 - - - +
1325 GLU* 3.0 43.7 + - + +
2735 PHE* 4.8 8.7 - - + -
2825 THR* 5.4 0.2 + - - -
2835 HIS* 4.7 1.6 - - - -
2845 TRP* 3.8 24.2 - - + -
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Residues in contact with THR 43 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 MET 3.3 8.8 + - - -
375 LEU* 4.1 1.5 - - + -
395 ASP 3.3 3.4 + - - -
425 ARG* 1.3 104.5 + - - +
445 LEU* 1.3 58.1 + - - +
465 TYR* 3.1 7.7 + - - +
475 ARG* 2.8 26.1 + - - +
715 ILE* 4.0 12.3 - - + -
725 LEU* 4.7 4.3 - - + -
755 PHE* 3.8 17.3 - - + -
1906 TYR* 3.0 42.3 + - + -
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Residues in contact with LEU 44 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405 THR* 3.0 35.9 + - + +
415 VAL* 4.6 1.3 - - - +
435 THR* 1.3 72.3 - - - +
455 SER* 1.3 58.0 + - - +
475 ARG* 3.0 36.9 + - + +
485 ASN* 2.7 42.1 + - - +
755 PHE* 6.1 0.2 - - - -
1906 TYR* 4.0 27.1 - - + -
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Residues in contact with SER 45 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415 VAL* 2.7 27.9 + - - +
425 ARG 3.5 3.6 - - - -
445 LEU* 1.3 74.8 - - - +
465 TYR* 1.3 62.8 + - - +
485 ASN* 5.0 0.7 - - - -
495 ALA* 2.9 26.5 + - - +
2625 PHE* 4.0 9.6 - - - -
2715 VAL* 3.7 15.1 - - - +
2725 GLU 4.6 2.8 + - - -
2735 PHE* 3.6 36.0 - - - +
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Residues in contact with TYR 46 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425 ARG* 3.1 25.0 + - + -
435 THR* 3.1 6.3 + - - +
455 SER* 1.3 73.7 - - - +
475 ARG* 1.3 66.2 + - - +
495 ALA* 3.8 1.9 - - - +
505 ILE* 3.0 31.7 + - + +
725 LEU* 3.5 41.3 - - + -
1305 ILE* 5.3 2.9 - - + -
1315 SER 2.9 22.0 + - - -
1325 GLU* 3.6 19.6 - - + -
1345 MET* 3.4 14.0 - - + +
1625 PHE* 3.4 26.0 - + + -
1635 PRO* 3.1 10.9 - - + +
2625 PHE* 3.5 30.3 - + - -
2735 PHE* 4.4 12.8 - + - -
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Residues in contact with ARG 47 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435 THR 2.8 16.8 + - - +
445 LEU* 3.0 31.9 + - - +
465 TYR* 1.3 70.3 - - - +
485 ASN* 1.3 85.0 + - - +
505 ILE* 2.8 23.0 + - - +
515 ILE* 2.9 37.5 + - + +
755 PHE* 3.6 47.4 - - + -
795 HIS* 4.9 2.7 - - + -
1906 TYR* 4.6 16.6 + - - +
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Residues in contact with ASN 48 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445 LEU* 2.7 32.7 + - - +
455 SER* 4.4 1.8 - - - +
475 ARG* 1.3 103.3 + - - +
495 ALA* 1.3 60.6 + - - +
515 ILE* 3.8 14.9 - - - +
525 GLN* 3.2 22.0 + - - +
2715 VAL* 4.0 17.0 - - + +
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Residues in contact with ALA 49 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 SER 2.9 20.8 + - - +
465 TYR 3.8 3.4 - - - +
485 ASN* 1.3 74.8 - - - +
505 ILE* 1.3 65.0 + - - +
525 GLN* 3.1 15.7 + - - +
535 ASN* 3.1 18.3 + - - +
1625 PHE* 4.3 6.1 - - + -
2625 PHE* 3.6 40.6 - - + -
2635 PRO 5.6 0.4 - - - +
2715 VAL* 4.0 12.4 - - + +
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Residues in contact with ILE 50 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465 TYR* 3.0 27.2 + - + +
475 ARG* 2.8 9.0 + - - +
495 ALA* 1.3 69.8 - - - +
515 ILE* 1.3 57.7 + - - +
535 ASN* 3.1 4.4 + - - +
545 LYS* 2.9 26.5 + - - -
575 PHE* 3.6 32.8 - - + -
725 LEU* 4.3 11.2 - - + +
755 PHE* 3.8 39.9 - - + +
765 ALA* 4.3 4.7 - - - +
795 HIS* 4.2 12.1 - - + +
1305 ILE* 4.4 21.3 - - + -
1625 PHE* 4.6 14.4 - - + -
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Residues in contact with ILE 51 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475 ARG* 2.9 47.3 + - + +
485 ASN* 3.8 17.0 - - - +
505 ILE* 1.3 75.2 - - - +
525 GLN* 1.3 62.8 + - - +
545 LYS* 3.0 43.4 + - + +
795 HIS* 3.7 31.0 - - + +
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Residues in contact with GLN 52 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485 ASN 3.2 10.9 + - - +
495 ALA* 3.1 10.6 + - - +
515 ILE* 1.3 79.3 - - - +
535 ASN* 1.3 60.1 + - - +
545 LYS* 3.6 1.4 + - - +
555 ASP* 4.8 4.9 + - - +
565 LEU* 5.4 0.3 - - - +
2625 PHE* 6.2 0.2 - - - +
2635 PRO 4.5 3.3 - - - +
2645 ALA* 3.6 21.3 - - - +
2655 PRO* 4.0 16.9 - - + +
2685 LYS* 4.2 35.0 - - + +
2695 ARG 3.4 23.1 + - - +
2715 VAL* 4.0 22.9 + - - +
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Residues in contact with ASN 53 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 ALA* 3.1 14.5 + - - +
505 ILE 3.1 9.4 + - - +
525 GLN* 1.3 80.1 + - - +
545 LYS* 1.3 62.1 + - - -
555 ASP 3.2 3.6 - - - -
565 LEU* 2.8 20.0 + - + +
575 PHE* 2.8 25.8 + - + -
1285 ILE* 6.1 0.2 - - + -
1605 LEU* 3.7 20.1 - - - +
1625 PHE* 3.4 25.5 - - + -
2635 PRO 3.1 25.4 + - - +
2645 ALA* 4.3 1.4 - - - -
2655 PRO* 3.8 17.6 - - - +
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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
------------------------------------------------------------
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