Contacts of the helix formed by residues 53 - 64 (chain q) in PDB entry 3J7Y
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 GLY 53 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39q TRP* 5.8 0.9 - - - -
49q ARG 3.7 3.5 + - - -
50q TRP* 3.6 9.0 + - - -
51q GLN 3.3 3.1 - - - +
52q LEU* 1.3 93.1 - - - +
54q PRO* 1.4 73.4 - - - +
55q ARG* 3.4 2.9 - - - -
56q TYR* 3.6 14.9 - - - +
57q ALA* 3.6 7.4 + - - +
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Residues in contact with PRO 54 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53q GLY* 1.4 82.7 - - - +
55q ARG* 1.3 63.0 + - + +
56q TYR 3.2 0.7 - - - -
57q ALA* 3.2 10.6 + - + +
58q ALA* 2.9 28.6 + - - +
74q SER* 4.8 15.0 + - - +
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Residues in contact with ARG 55 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1759A U 4.5 17.4 + - - -
1760A G 6.0 5.6 - - - -
196M ARG* 4.7 6.5 + - - +
198M GLN* 3.5 38.4 + - - +
50q TRP 5.8 0.9 - - - +
53q GLY* 5.2 0.9 - - - -
54q PRO* 1.3 83.0 - - + +
56q TYR* 1.3 56.8 + - - +
58q ALA* 3.2 10.2 + - - +
59q LYS* 2.9 41.8 + - - +
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Residues in contact with TYR 56 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38q ARG* 2.7 28.7 + - - +
39q TRP* 4.8 9.2 - + - -
40q PRO* 4.0 9.9 - - + -
50q TRP* 3.4 32.6 + + - +
51q GLN* 3.0 59.1 + - + +
53q GLY 3.6 9.1 + - - +
54q PRO 3.2 0.2 - - - -
55q ARG* 1.3 78.8 - - - +
57q ALA* 1.3 57.6 + - - +
59q LYS* 3.2 12.1 + - + +
60q GLN* 2.7 74.7 + - - -
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Residues in contact with ALA 57 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39q TRP* 3.5 34.1 - - + -
53q GLY 3.6 6.5 + - - +
54q PRO* 3.2 15.2 + - + +
56q TYR* 1.3 78.7 - - - +
58q ALA* 1.3 57.9 + - - +
60q GLN* 3.2 4.6 + - - +
61q PHE 2.9 24.4 + - - -
70q VAL* 3.2 23.7 - - + +
74q SER* 5.8 2.7 - - - +
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Residues in contact with ALA 58 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M ARG 4.1 6.5 - - - +
197M GLY* 4.3 8.5 - - - +
198M GLN* 6.5 0.4 - - + -
54q PRO 2.9 12.6 + - - +
55q ARG* 3.3 13.9 - - - +
57q ALA* 1.3 75.5 - - - +
59q LYS* 1.3 58.1 + - - +
61q PHE* 3.2 7.7 + - - +
62q ALA* 2.9 28.9 + - - +
70q VAL* 5.2 0.9 - - - -
75q LEU* 3.6 29.4 - - + -
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Residues in contact with LYS 59 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1760A G 3.8 41.0 + - - +
195M LEU 3.6 10.5 - - - +
196M ARG* 3.4 44.2 + - - +
55q ARG* 2.9 26.2 + - - +
56q TYR* 3.4 15.9 - - + +
58q ALA* 1.3 75.5 - - - +
60q GLN* 1.3 61.3 + - - +
62q ALA* 3.2 4.2 + - - +
63q ARG* 2.9 40.8 + - - +
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Residues in contact with GLN 60 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37q PRO* 3.6 28.3 - - + -
38q ARG* 4.1 8.1 + - - +
39q TRP* 4.3 16.6 - - + +
56q TYR* 2.7 83.9 + - - -
57q ALA* 3.2 8.6 + - - +
59q LYS* 1.3 78.8 - - - +
61q PHE* 1.3 57.3 + - - +
63q ARG* 3.2 8.4 + - - +
64q TYR* 2.9 46.1 + - + +
65q GLY 4.8 0.2 - - - +
69q GLY* 5.0 2.7 - - - -
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Residues in contact with PHE 61 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M GLY* 5.3 0.7 - - - -
274M VAL* 4.2 13.5 - - + -
275M VAL 5.9 0.2 - - - -
276M ASN* 3.6 30.1 - - + +
283M LEU* 3.6 26.2 - - + -
57q ALA 2.9 12.9 + - - +
58q ALA* 3.4 9.2 - - - +
60q GLN* 1.3 74.5 - - - +
62q ALA* 1.3 71.6 + - + +
65q GLY* 3.2 39.3 + - - -
66q ALA* 3.6 22.2 - - + -
69q GLY* 4.5 3.4 - - - -
70q VAL* 3.7 31.6 - - + +
72q PRO* 4.5 4.0 - - + -
75q LEU* 3.3 36.8 - - + -
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Residues in contact with ALA 62 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PHE 3.4 17.5 - - - +
195M LEU* 2.9 34.0 - - - +
197M GLY* 3.6 9.6 - - - -
275M VAL 5.5 4.5 - - - +
276M ASN* 4.0 11.3 - - - +
277M MET* 4.4 9.0 + - - +
278M ALA* 4.3 7.3 + - - +
58q ALA 2.9 13.6 + - - +
59q LYS 3.4 3.4 - - - +
61q PHE* 1.3 87.5 - - + +
63q ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 63 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F LEU* 6.4 0.2 - - - +
195M LEU* 4.7 29.3 - - + +
278M ALA* 3.3 19.4 + - - +
33q ARG* 3.5 38.9 - - - +
59q LYS* 2.9 26.7 + - + +
60q GLN* 3.5 11.0 - - - +
62q ALA* 1.3 77.6 - - - +
64q TYR* 1.3 97.2 + - + +
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Residues in contact with TYR 64 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278M ALA* 3.2 15.6 - - - +
279M ASP* 4.2 5.7 - - - +
33q ARG* 5.4 1.6 + - - +
34q ARG 4.0 9.1 + - - -
35q PRO 3.2 28.9 - - - -
36q GLY 3.6 12.0 + - - -
37q PRO* 3.6 33.9 - - + +
38q ARG* 4.7 3.1 + - - +
60q GLN* 2.9 32.5 + - + +
63q ARG* 1.3 114.8 + - + +
65q GLY* 1.3 60.1 + - - +
68q SER* 3.7 25.2 + - - +
69q GLY 5.0 0.4 - - - +
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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