Contacts of the helix formed by residues 49 - 66 (chain Z) in PDB entry 3J9X
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 49 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518 A 3.9 27.1 - - + +
10Y TYR* 3.8 10.1 - - + -
13Y ARG* 3.7 27.6 - - + +
45Z PHE* 3.0 63.6 + - + +
48Z ASN* 1.3 71.7 - - - +
50Z PRO* 1.4 64.5 - - + +
51Z LYS 3.0 3.6 - - - -
52Z PHE* 2.8 26.8 + - - +
53Z THR 3.2 6.8 + - - -
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Residues in contact with PRO 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y TYR* 3.5 39.2 - - + +
46Z GLN 3.1 25.4 - - - +
47Z THR 3.7 6.1 - - - +
48Z ASN 3.4 2.5 - - - -
49Z VAL* 1.4 96.2 - - + +
51Z LYS* 1.3 65.9 + - + +
53Z THR* 3.7 4.6 - - - +
54Z SER* 3.1 24.6 + - - -
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Residues in contact with LYS 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Z THR* 3.4 27.5 + - - +
48Z ASN* 3.0 34.5 + - - +
49Z VAL 2.9 0.4 + - - -
50Z PRO* 1.3 80.4 - - + +
52Z PHE* 1.3 63.6 + - + +
54Z SER* 2.9 19.7 + - - -
55Z VAL* 3.4 12.5 - - - +
84Z ALA* 6.2 0.2 - - - -
88Z ASN* 3.8 30.8 + - - +
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Residues in contact with PHE 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508 T 3.6 24.0 - - + +
1518 A 3.5 30.1 - - - +
13Y ARG* 4.6 5.6 - - - +
48Z ASN* 3.1 28.9 - - + -
49Z VAL* 2.8 8.0 + - - +
51Z LYS* 1.3 77.2 - - + +
53Z THR* 1.3 66.3 + - - +
54Z SER 3.2 1.3 - - - -
55Z VAL* 3.1 7.9 + - - +
56Z ASN* 3.0 26.8 + - - +
81Z LEU* 3.5 44.8 - - + +
84Z ALA* 3.6 13.7 - - + -
85Z ARG* 3.5 13.9 - - - -
88Z ASN* 3.4 28.0 - - - -
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Residues in contact with THR 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y ARG 4.8 2.2 - - - +
9Y SER* 4.3 5.8 - - - -
10Y TYR* 3.5 41.2 - - + +
13Y ARG* 2.8 37.3 + - - +
49Z VAL 3.2 8.3 + - - -
50Z PRO* 3.3 8.3 + - - -
52Z PHE* 1.3 78.8 - - - +
54Z SER* 1.3 61.9 + - - +
56Z ASN* 3.1 18.3 + - + +
57Z GLU* 3.1 13.2 + - + +
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Residues in contact with SER 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Z PRO 3.1 12.1 + - - -
51Z LYS* 2.9 22.3 + - - -
53Z THR* 1.3 77.3 - - - +
55Z VAL* 1.3 63.4 + - - +
57Z GLU* 3.4 10.5 + - - +
58Z ASN* 3.2 28.9 + - - +
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Residues in contact with VAL 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Z LYS 3.4 17.7 - - - +
52Z PHE* 3.1 13.8 + - - +
54Z SER* 1.3 80.5 + - - +
56Z ASN* 1.3 61.2 + - - +
58Z ASN* 3.3 4.7 + - - +
59Z VAL* 2.8 52.3 + - + +
77Z GLN* 5.4 0.7 - - - +
80Z GLY 4.5 7.9 - - - +
81Z LEU* 4.5 12.6 - - + +
84Z ALA* 4.2 17.7 - - + -
124Z ILE* 6.1 1.1 - - - -
125Z ILE* 4.0 26.0 - - + -
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Residues in contact with ASN 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007 T 5.2 4.9 + - - +
2017 A 4.4 31.6 + - - +
13Y ARG* 4.3 13.9 - - - +
52Z PHE* 3.0 16.9 + - - +
53Z THR* 3.1 15.3 + - + +
55Z VAL* 1.3 77.7 - - - +
57Z GLU* 1.3 57.1 + - - +
60Z SER* 2.9 33.4 + - - -
77Z GLN* 3.4 20.7 + - - +
81Z LEU* 3.4 29.7 - - - +
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Residues in contact with GLU 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Z THR* 3.1 11.3 + - + +
54Z SER* 3.7 10.7 - - - +
55Z VAL 3.2 0.6 - - - -
56Z ASN* 1.3 77.6 - - - +
58Z ASN* 1.3 70.2 + - - +
60Z SER* 3.6 3.9 - - - -
61Z ALA* 3.1 22.5 + - + +
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Residues in contact with ASN 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Z SER* 3.2 16.5 + - - +
55Z VAL* 4.0 2.2 - - - +
57Z GLU* 1.3 86.9 - - - +
59Z VAL* 1.3 66.2 + - - +
61Z ALA* 3.2 9.3 + - - +
62Z VAL* 3.1 26.3 + - - +
124Z ILE* 3.6 28.8 - - + +
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Residues in contact with VAL 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Z VAL* 2.8 42.0 + - + +
58Z ASN* 1.3 71.6 - - - +
60Z SER* 1.3 63.0 + - - +
62Z VAL* 3.1 9.6 + - - +
63Z LEU* 3.0 30.0 + - + +
76Z TYR 4.4 7.2 - - - +
77Z GLN* 3.3 26.9 - - - +
80Z GLY* 5.0 1.3 - - - -
121Z VAL* 4.1 37.7 - - + +
124Z ILE* 4.9 8.7 - - + -
125Z ILE* 4.6 6.1 - - + -
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Residues in contact with SER 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2017 A 4.8 0.9 - - - -
2027 T 2.9 20.1 + - - -
89X ARG 4.5 4.0 + - - -
90X ILE 4.9 2.1 + - - -
56Z ASN 2.9 21.4 + - - -
57Z GLU* 3.6 4.7 - - - -
59Z VAL* 1.3 78.0 - - - +
61Z ALA* 1.3 62.9 + - - +
63Z LEU* 3.1 4.0 + - - -
64Z THR* 3.0 10.3 + - - -
73Z ARG* 2.7 41.4 + - - +
77Z GLN* 3.5 8.2 - - - +
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Residues in contact with ALA 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X ILE 5.8 0.7 - - - -
57Z GLU* 3.1 14.9 + - + +
58Z ASN* 3.2 12.5 + - - +
60Z SER* 1.3 77.1 - - - +
62Z VAL* 1.3 63.3 + - + +
64Z THR* 3.2 10.0 + - - -
65Z GLN* 3.1 26.8 + - + +
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Residues in contact with VAL 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Z ASN 3.1 14.5 + - - +
59Z VAL* 3.1 10.1 + - + +
61Z ALA* 1.3 76.4 - - + +
63Z LEU* 1.3 63.2 + - + +
65Z GLN* 2.9 11.2 + - + +
66Z TYR* 2.9 51.5 + - + -
117Z VAL* 5.5 0.4 - - + +
120Z ALA* 3.8 18.2 - - + +
121Z VAL* 5.0 4.5 - - + +
124Z ILE* 3.7 32.3 - - + -
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Residues in contact with LEU 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z VAL* 3.0 33.8 + - + +
60Z SER* 3.1 7.6 + - - +
62Z VAL* 1.3 76.5 - - + +
64Z THR* 1.3 61.5 + - - +
66Z TYR* 3.2 2.7 + - - +
67Z GLY 3.0 4.2 + - - -
68Z ILE* 2.9 39.7 + - + +
73Z ARG* 3.5 48.5 - - + +
76Z TYR* 3.6 31.6 - - + -
77Z GLN* 4.0 10.3 - - - +
117Z VAL* 3.6 19.5 - - + -
121Z VAL* 5.0 2.7 - - + -
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Residues in contact with THR 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X ILE* 2.6 28.6 + - + +
91X GLY 3.6 13.7 - - - +
92X SER 3.4 27.1 - - - +
93X GLY* 4.5 1.8 - - - -
94X PRO* 3.3 4.0 - - + +
95X ALA* 3.2 20.2 + - + +
60Z SER 3.0 5.4 + - - -
61Z ALA* 3.4 11.2 - - - -
62Z VAL 3.1 0.2 - - - -
63Z LEU* 1.3 77.8 - - - +
65Z GLN* 1.3 64.9 + - - +
67Z GLY 3.1 9.7 + - - -
73Z ARG* 2.9 22.7 + - - +
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Residues in contact with GLN 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X SER 4.9 7.9 + - - -
93X GLY* 5.3 1.0 - - - -
94X PRO* 3.4 32.0 - - - +
61Z ALA* 3.1 17.5 + - + +
62Z VAL* 2.9 12.1 + - - +
64Z THR* 1.3 77.3 - - - +
66Z TYR* 1.3 63.5 + - + +
67Z GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X PRO* 4.7 0.7 - - - -
62Z VAL* 2.9 35.0 + - + +
63Z LEU* 3.2 5.6 + - - +
65Z GLN* 1.3 79.7 - - + +
67Z GLY* 1.3 61.7 + - - +
68Z ILE* 3.2 21.4 + - + +
116Z GLN* 3.2 42.6 + - + -
117Z VAL* 3.9 19.3 - - + -
120Z ALA* 3.5 30.5 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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