Contacts of the helix formed by residues 49 - 66 (chain n) 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 n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2358 A 3.9 27.6 - - + +
2368 T 5.2 0.2 - - - -
10m TYR* 3.8 9.6 - - + -
13m ARG* 3.7 27.1 - - - +
45n PHE* 3.0 63.4 + - + +
48n ASN* 1.3 71.3 - - - +
50n PRO* 1.4 61.0 - - + +
51n LYS 3.0 4.0 - - - -
52n PHE* 2.8 30.4 + - - +
53n THR 3.2 6.6 + - - -
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Residues in contact with PRO 50 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I PRO* 5.8 2.0 - - + -
9J SER* 6.4 2.5 - - - -
10J TYR* 4.1 20.6 - - + -
11J SER* 5.7 0.7 - - - -
10m TYR* 3.5 34.9 - - + +
46n GLN 3.1 25.8 - - - +
47n THR 3.7 6.5 - - - +
48n ASN 3.4 2.0 - - - -
49n VAL* 1.4 96.2 - - + +
51n LYS* 1.3 66.1 + - + +
53n THR* 3.7 4.9 - - - +
54n SER* 3.1 23.7 + - - -
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Residues in contact with LYS 51 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47n THR* 3.4 27.3 + - - +
48n ASN* 3.0 34.1 + - - +
49n VAL 2.9 0.2 + - - -
50n PRO* 1.3 80.4 - - + +
52n PHE* 1.3 63.3 + - + +
54n SER* 2.9 19.7 + - - -
55n VAL* 3.4 12.3 - - - +
84n ALA* 5.7 0.4 - - - +
88n ASN* 3.8 30.1 + - - +
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Residues in contact with PHE 52 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2348 T 3.6 23.8 - - + +
2358 A 3.5 30.1 - - - +
13m ARG* 4.6 5.4 - - - +
48n ASN* 3.1 28.3 - - + -
49n VAL* 2.8 7.5 + - - +
51n LYS* 1.3 76.6 - - + +
53n THR* 1.3 67.2 + - - +
54n SER 3.2 1.3 - - - -
55n VAL* 3.1 7.8 + - + +
56n ASN* 3.0 27.8 + - - +
81n LEU* 3.5 45.5 - - + +
84n ALA* 3.6 13.7 - - + -
85n ARG* 3.5 13.9 - - - -
88n ASN* 3.4 28.0 - - - -
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Residues in contact with THR 53 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8m ARG 4.8 2.5 - - - +
9m SER* 4.3 4.9 - - - -
10m TYR* 3.5 43.3 - - + +
13m ARG* 2.8 36.6 + - - +
49n VAL 3.2 7.9 + - - -
50n PRO* 3.3 7.8 + - - -
52n PHE* 1.3 78.1 - - - +
54n SER* 1.3 62.2 + - - +
56n ASN* 3.1 18.1 + - + +
57n GLU* 3.1 13.4 + - + +
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Residues in contact with SER 54 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I PRO 5.3 1.6 - - - -
54I SER* 3.3 35.8 - - - -
58I ASN* 5.3 5.3 + - - -
50n PRO 3.1 12.3 + - - -
51n LYS* 2.9 22.0 + - - -
53n THR* 1.3 76.6 - - - +
55n VAL* 1.3 63.0 + - - +
57n GLU* 3.4 10.0 + - - +
58n ASN* 3.2 28.8 + - - +
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Residues in contact with VAL 55 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51n LYS 3.4 17.9 - - - +
52n PHE* 3.1 13.6 + - - +
54n SER* 1.3 84.1 + - - +
56n ASN* 1.3 58.5 - - - +
58n ASN* 3.3 3.9 + - - +
59n VAL* 2.8 53.0 + - + +
77n GLN* 5.4 0.9 - - - +
80n GLY 4.5 8.3 - - - +
81n LEU* 4.5 12.6 - - + +
84n ALA* 4.2 17.7 - - + -
124n ILE* 6.1 1.3 - - - -
125n ILE* 4.0 25.8 - - + -
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Residues in contact with ASN 56 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167 T 5.2 4.9 + - - +
1177 A 4.4 31.0 + - - +
13m ARG* 4.3 14.1 - - - +
52n PHE 3.0 15.9 + - - -
53n THR* 3.1 15.2 + - + +
55n VAL* 1.3 77.5 - - - +
57n GLU* 1.3 57.7 + - - +
60n SER* 2.9 33.5 + - - -
77n GLN* 3.4 22.1 + - - +
81n LEU* 3.4 30.9 - - - +
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Residues in contact with GLU 57 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LYS* 4.2 31.4 - - - +
54I SER* 5.7 0.3 + - - -
87I LEU* 5.8 3.6 - - - +
88I ASN* 5.2 4.3 - - - +
53n THR* 3.1 12.0 + - + +
54n SER* 3.7 10.8 - - - +
55n VAL 3.2 0.2 - - - -
56n ASN* 1.3 76.8 - - - +
58n ASN* 1.3 70.1 + - - +
60n SER* 3.6 4.1 - - - -
61n ALA* 3.1 22.9 + - + +
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Residues in contact with ASN 58 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I SER* 5.5 4.8 + - - -
58I ASN* 4.2 17.8 - - - +
124I ILE* 4.3 9.8 + - - +
125I ILE* 4.2 17.2 + - - +
54n SER* 3.2 15.7 + - - +
55n VAL* 4.0 2.2 - - - +
57n GLU* 1.3 86.1 - - - +
59n VAL* 1.3 65.4 + - - +
61n ALA* 3.2 8.3 + - - +
62n VAL* 3.1 25.7 + - - +
124n ILE* 3.6 28.0 - - + +
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Residues in contact with VAL 59 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55n VAL* 2.8 41.3 + - + +
58n ASN* 1.3 72.9 - - - +
60n SER* 1.3 63.3 + - - +
62n VAL* 3.1 9.3 + - - +
63n LEU* 3.0 31.0 + - + +
76n TYR 4.4 7.2 - - - +
77n GLN* 3.3 27.4 - - - +
80n GLY* 5.0 1.3 - - - -
121n VAL* 4.1 36.8 - - + +
124n ILE* 4.9 8.7 - - + -
125n ILE* 4.6 7.0 - - + -
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Residues in contact with SER 60 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177 A 4.8 1.1 - - - -
1187 T 2.9 19.4 + - - -
89l ARG 4.5 4.2 + - - -
90l ILE 4.9 1.6 + - - -
56n ASN 2.9 21.8 + - - -
57n GLU* 3.6 5.4 - - - -
59n VAL* 1.3 78.0 - - - +
61n ALA* 1.3 62.4 + - - +
63n LEU* 3.1 3.6 + - - -
64n THR* 3.0 10.3 + - - -
73n ARG* 2.7 43.7 + - - +
77n GLN* 3.5 8.9 - - - +
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Residues in contact with ALA 61 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I THR 5.9 2.9 - - - +
90l ILE 5.8 0.4 - - - -
57n GLU* 3.1 15.1 + - + +
58n ASN* 3.2 13.0 + - - +
60n SER* 1.3 76.5 - - - +
62n VAL* 1.3 62.6 + - + +
64n THR* 3.2 10.2 + - - +
65n GLN* 3.1 26.3 + - + +
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Residues in contact with VAL 62 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I THR 5.0 8.7 - - - +
127I GLY* 5.1 1.8 - - - -
58n ASN 3.1 14.5 + - - +
59n VAL* 3.1 9.6 + - + +
61n ALA* 1.3 76.2 - - + +
63n LEU* 1.3 62.8 + - + +
65n GLN* 2.9 12.1 + - + +
66n TYR* 2.9 50.3 + - + -
117n VAL* 5.5 0.4 - - + -
120n ALA* 3.8 18.6 - - + +
121n VAL* 5.0 4.3 - - + +
124n ILE* 3.7 33.0 - - + -
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Residues in contact with LEU 63 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59n VAL* 3.0 33.4 + - + +
60n SER* 3.1 7.8 + - - +
62n VAL* 1.3 76.5 - - + +
64n THR* 1.3 60.4 + - - +
66n TYR* 3.2 3.0 + - - +
67n GLY 3.0 4.3 + - - -
68n ILE* 2.9 39.3 + - + +
73n ARG* 3.5 47.6 - - + +
76n TYR* 3.6 32.5 - - + -
77n GLN* 4.0 10.3 - - - +
117n VAL* 3.6 18.8 - - + -
121n VAL* 5.0 2.7 - - + -
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Residues in contact with THR 64 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90l ILE* 2.6 28.5 + - + +
91l GLY 3.6 13.5 - - - +
92l SER 3.4 27.1 - - - +
93l GLY* 4.5 1.8 - - - -
94l PRO* 3.3 4.0 - - + +
95l ALA* 3.2 20.4 + - + +
60n SER 3.0 5.6 + - - -
61n ALA* 3.4 11.4 - - - -
62n VAL 3.1 0.2 - - - -
63n LEU* 1.3 77.8 - - - +
65n GLN* 1.3 63.6 + - - +
67n GLY 3.1 10.0 + - - -
73n ARG* 2.9 23.5 + - - +
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Residues in contact with GLN 65 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER* 4.4 17.4 + - - -
126I THR 6.0 0.9 - - - +
133I VAL* 3.9 20.6 - - - +
134I SER* 3.0 41.3 + - - +
92l SER 4.9 7.9 + - - -
93l GLY* 5.3 1.2 - - - -
94l PRO* 3.4 31.0 - - - +
61n ALA* 3.1 17.5 + - + +
62n VAL* 2.9 12.2 + - - +
64n THR* 1.3 77.2 - - - +
66n TYR* 1.3 64.7 + - + +
67n GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I SER* 5.9 4.9 - - - -
94l PRO* 4.7 0.7 - - - -
62n VAL* 2.9 33.2 + - + +
63n LEU* 3.2 5.8 + - - +
65n GLN* 1.3 80.5 - - + +
67n GLY* 1.3 62.7 + - - +
68n ILE* 3.2 21.4 + - + +
116n GLN* 3.2 41.7 + - + -
117n VAL* 3.9 19.7 - - + -
120n ALA* 3.5 31.0 - - + +
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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