Contacts of the helix formed by residues 49 - 61 (chain 1) in PDB entry 6Q8W
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 THR 49 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471 GLU 5.1 2.9 - - - +
481 LYS* 1.3 76.9 - - - +
501 PRO* 1.3 70.9 - - + +
511 ASP* 4.1 7.4 + - - +
521 GLU* 2.8 48.6 + - - +
531 VAL* 3.1 11.8 + - - +
1231 TYR* 3.5 4.3 - - - +
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Residues in contact with PRO 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 THR* 1.3 89.3 - - + +
511 ASP* 1.3 63.0 + - - +
531 VAL* 3.1 14.3 - - + +
541 ILE* 3.0 28.8 + - - +
1231 TYR* 3.6 32.1 - - + +
1241 ALA* 3.3 22.9 - - - +
1261 ARG* 3.5 30.1 - - + +
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Residues in contact with ASP 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 THR* 3.2 7.4 - - - +
501 PRO* 1.3 79.0 - - - +
521 GLU* 1.3 58.2 + - + +
541 ILE* 3.9 6.0 - - - +
551 GLU* 2.9 36.9 + - + +
811 LYS* 4.0 25.3 - - - +
1261 ARG* 4.9 8.8 + - - -
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Residues in contact with GLU 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 GLU 4.6 2.3 - - - +
481 LYS* 3.4 36.1 + - + +
491 THR* 2.8 46.3 + - - +
511 ASP* 1.3 78.6 - - + +
531 VAL* 1.3 57.1 + - - +
551 GLU* 3.8 4.9 - - - +
561 GLU* 2.9 31.6 + - - +
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Residues in contact with VAL 53 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 VAL* 4.7 12.3 - - + -
481 LYS* 4.7 1.7 - - + +
491 THR 3.1 5.9 + - - +
501 PRO* 3.1 31.2 - - + +
521 GLU* 1.3 75.5 - - - +
541 ILE* 1.3 59.0 + - - +
561 GLU* 3.4 7.0 - - - +
571 VAL* 3.1 25.7 + - + +
761 TRP* 4.7 6.1 - - + -
1201 LEU* 4.3 17.7 - - + +
1231 TYR* 4.2 9.9 - - + -
1241 ALA* 3.6 21.5 - - + -
2271 VAL* 5.8 0.9 - - + -
2311 MET* 3.8 32.3 - - + -
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Residues in contact with ILE 54 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501 PRO 3.0 18.7 + - - +
511 ASP* 3.9 5.4 - - - +
531 VAL* 1.3 74.5 - - - +
551 GLU* 1.3 61.9 + - + +
561 GLU 3.1 1.3 - - - -
571 VAL* 3.2 4.4 + - - +
581 LYS* 2.9 30.2 + - - +
731 GLY* 3.7 22.8 - - - +
761 TRP* 3.5 34.5 - - + +
771 SER* 4.5 10.1 - - - +
811 LYS* 3.5 31.4 - - - +
1241 ALA* 3.4 29.2 - - + +
1251 ILE* 4.7 1.1 - - + -
1261 ARG* 4.9 0.2 - - - +
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Residues in contact with GLU 55 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 ASP* 2.9 21.6 + - + +
521 GLU* 3.9 4.7 - - - +
541 ILE* 1.3 77.3 - - + +
561 GLU* 1.3 57.0 + - - +
581 LYS* 3.2 42.8 + - - +
591 ARG* 2.9 67.3 + - - +
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Residues in contact with GLU 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481 LYS* 4.2 18.9 + - - -
521 GLU 2.9 19.2 + - - +
531 VAL* 3.4 11.4 - - - +
551 GLU* 1.3 76.5 - - - +
571 VAL* 1.3 58.0 + - - +
591 ARG* 3.2 11.9 + - - +
601 SER* 2.9 26.0 + - - -
2301 ILE* 4.2 5.5 - - + +
2311 MET* 3.8 27.6 - - + -
2351 ALA* 3.2 34.1 + - + +
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Residues in contact with VAL 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531 VAL* 3.1 20.6 + - + +
541 ILE 3.2 6.3 + - - +
561 GLU* 1.3 74.0 - - + +
581 LYS* 1.3 66.0 + - - +
601 SER* 2.4 33.3 + - - +
611 GLY 3.7 2.1 + - - -
621 LEU* 4.0 18.7 + - + +
721 THR* 3.0 28.9 - - - +
731 GLY* 4.1 8.9 + - - +
761 TRP* 4.0 23.3 - - + -
2271 VAL* 5.3 9.9 - - + -
2301 ILE* 4.7 12.6 - - + -
2311 MET* 5.0 2.7 - - - -
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Residues in contact with LYS 58 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541 ILE* 2.9 18.1 + - - +
551 GLU* 3.2 34.6 + - - +
561 GLU 3.2 0.2 - - - -
571 VAL* 1.3 78.3 - - - +
591 ARG* 1.3 60.2 + - + +
611 GLY* 3.4 10.0 + - - -
711 PRO* 6.1 5.2 - - + +
731 GLY* 3.9 24.8 - - - +
741 LEU* 4.5 16.9 - - + +
771 SER* 4.1 18.0 + - - -
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Residues in contact with ARG 59 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551 GLU* 2.9 50.5 + - - +
561 GLU* 3.6 10.0 - - - +
581 LYS* 1.3 72.1 - - + +
601 SER* 1.3 62.6 + - - +
611 GLY 3.1 4.4 + - - -
2351 ALA* 5.1 6.3 - - + +
2361 ASP* 5.5 1.9 - - - +
2391 ALA* 4.8 7.6 - - - +
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Residues in contact with SER 60 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561 GLU 2.9 13.1 + - - -
571 VAL* 2.4 28.9 + - - +
591 ARG* 1.3 76.4 - - - +
611 GLY* 1.3 61.0 + - - +
621 LEU* 3.1 18.6 + - - +
2301 ILE* 3.8 25.1 - - - -
2351 ALA* 4.4 17.7 - - - +
2381 PHE* 3.4 19.0 - - - -
2391 ALA* 4.1 8.6 - - - +
2471 LYS* 3.9 6.8 - - - +
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Residues in contact with GLY 61 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581 LYS 3.4 9.3 + - - -
591 ARG 3.1 7.7 + - - -
601 SER* 1.3 77.6 + - - +
621 LEU* 1.3 62.1 + - - +
631 ARG* 3.2 13.8 + - - +
651 ARG* 5.2 0.2 + - - -
711 PRO* 6.1 2.5 - - - -
2451 GLN 5.0 0.7 - - - +
2471 LYS* 3.5 30.6 + - - +
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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
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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