Contacts of the helix formed by residues 49 - 66 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 A 3.9 27.8 - - + +
10A TYR* 3.8 10.5 - - + -
13A ARG* 3.7 26.7 - - - +
45B PHE* 3.0 62.9 + - + +
48B ASN* 1.3 71.5 - - - +
50B PRO* 1.4 60.1 - - + +
51B LYS 3.0 4.3 - - - -
52B PHE* 2.8 31.0 + - - +
53B THR 3.2 6.8 + - - -
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 37.7 - - + -
46B GLN 3.1 24.5 - - - +
47B THR 3.7 6.5 - - - +
48B ASN 3.4 2.5 - - - -
49B VAL* 1.4 96.2 - - + +
51B LYS* 1.3 65.6 + - + +
53B THR* 3.7 5.6 - - - +
54B SER* 3.1 24.6 + - - -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.4 28.0 + - - +
48B ASN* 3.0 33.3 + - - +
49B VAL 2.9 0.4 + - - -
50B PRO* 1.3 80.9 - - + +
52B PHE* 1.3 63.7 + - + +
54B SER* 2.9 19.9 + - - -
55B VAL* 3.4 11.8 - - - +
84B ALA* 5.7 0.4 - - - +
88B ASN* 3.8 29.7 + - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68 T 3.6 24.7 - - + +
78 A 3.5 28.3 - - - +
13A ARG* 4.6 5.8 - - - +
48B ASN* 3.1 28.7 - - + -
49B VAL* 2.8 8.0 + - - +
51B LYS* 1.3 77.5 - - + +
53B THR* 1.3 66.5 + - - +
54B SER 3.2 0.4 - - - -
55B VAL* 3.1 7.3 + - - +
56B ASN* 3.0 27.6 + - - +
81B LEU* 3.5 44.1 - - + +
84B ALA* 3.6 13.5 - - + -
85B ARG* 3.5 14.1 - - - -
88B ASN* 3.4 28.9 - - - -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG 4.8 2.5 - - - +
9A SER* 4.3 5.8 - - - -
10A TYR* 3.5 42.9 - - + +
13A ARG* 2.8 35.6 + - - +
49B VAL 3.2 8.5 + - - -
50B PRO* 3.7 8.1 - - - -
52B PHE* 1.3 78.9 - - - +
54B SER* 1.3 62.6 + - - +
56B ASN* 3.1 17.9 + - + +
57B GLU* 3.1 13.3 + - + +
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO 3.1 11.8 + - - -
51B LYS* 2.9 22.2 + - - -
53B THR* 1.3 76.8 - - - +
55B VAL* 1.3 62.9 + - - +
57B GLU* 3.4 10.2 + - - +
58B ASN* 3.2 29.4 + - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS 3.4 17.9 - - - +
52B PHE* 3.1 12.9 + - - +
54B SER* 1.3 83.9 + - - +
56B ASN* 1.3 59.7 + - - +
58B ASN* 3.3 4.1 + - - +
59B VAL* 2.8 53.0 + - + +
77B GLN* 5.4 0.7 - - - +
80B GLY 4.5 8.3 - - - +
81B LEU* 4.5 12.3 - - + +
84B ALA* 4.2 17.5 - - + -
124B ILE* 6.1 0.9 - - - -
125B ILE* 4.0 25.4 - - + -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3447 T 5.2 4.4 + - - +
3457 A 4.4 30.7 + - - +
13A ARG* 4.3 14.5 - - - +
52B PHE* 3.0 16.2 + - - +
53B THR* 3.1 15.9 + - + +
55B VAL* 1.3 77.9 - - - +
57B GLU* 1.3 56.8 + - - +
60B SER* 2.9 33.4 + - - -
77B GLN* 3.4 21.3 + - - +
81B LEU* 3.4 30.5 - - - +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 3.1 12.8 + - + +
54B SER* 3.7 11.2 - - - +
55B VAL 3.2 0.2 - - - -
56B ASN* 1.3 76.8 - - - +
58B ASN* 1.3 69.5 + - - +
60B SER* 3.6 4.1 - - - -
61B ALA* 3.1 23.2 + - + +
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 3.2 16.5 + - - +
55B VAL* 4.0 2.4 - - - +
57B GLU* 1.3 85.8 - - - +
59B VAL* 1.3 66.6 + - - +
61B ALA* 3.2 9.4 + - - +
62B VAL* 3.1 25.8 + - - +
124B ILE* 3.6 28.6 - - + +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 2.8 42.4 + - + +
58B ASN* 1.3 72.0 - - - +
60B SER* 1.3 62.7 + - - +
62B VAL* 3.1 9.5 + - - +
63B LEU* 3.0 31.1 + - + +
76B TYR 4.4 6.7 - - - +
77B GLN* 3.3 27.4 - - - +
80B GLY* 5.0 1.6 - - - -
121B VAL* 4.1 37.2 - - + +
124B ILE* 4.9 9.4 - - + -
125B ILE* 4.6 6.1 - - + -
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3457 A 4.8 1.1 - - - -
3467 T 2.9 20.1 + - - -
56B ASN 2.9 21.6 + - - -
57B GLU* 3.6 5.6 - - - -
59B VAL* 1.3 77.1 - - - +
61B ALA* 1.3 61.8 + - - +
63B LEU* 3.1 3.5 + - - -
64B THR* 3.0 10.4 + - - -
73B ARG* 2.7 42.2 + - - +
77B GLN* 3.5 8.9 - - - +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.1 14.9 + - + +
58B ASN* 3.2 12.8 + - - +
60B SER* 1.3 76.1 - - - +
62B VAL* 1.3 63.5 + - + +
64B THR* 3.2 10.0 + - - -
65B GLN* 3.1 25.7 + - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN 3.1 13.9 + - - +
59B VAL* 3.1 9.4 + - - +
61B ALA* 1.3 76.6 - - + +
63B LEU* 1.3 63.6 + - + +
65B GLN* 2.9 11.7 + - + +
66B TYR* 2.9 50.6 + - + -
117B VAL* 5.5 0.4 - - + +
120B ALA* 3.8 17.9 - - + +
121B VAL* 5.0 4.7 - - + +
124B ILE* 3.7 33.0 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 3.0 34.1 + - + +
60B SER* 3.1 7.4 + - - +
62B VAL* 1.3 76.5 - - + +
64B THR* 1.3 61.1 + - - +
66B TYR* 3.2 3.1 + - - +
67B GLY 3.0 4.3 + - - -
68B ILE* 2.9 39.1 + - + -
73B ARG* 3.5 46.7 - - + +
76B TYR* 3.6 32.3 - - + -
77B GLN* 4.0 11.0 - - - +
117B VAL* 3.6 19.1 - - + -
121B VAL* 5.0 3.4 - - + -
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER 3.0 5.7 + - - -
61B ALA* 3.4 11.1 - - - -
62B VAL 3.1 0.2 - - - -
63B LEU* 1.3 77.8 - - - +
65B GLN* 1.3 66.9 + - - +
67B GLY* 3.1 13.7 + - - -
68B ILE 4.8 0.9 - - - +
73B ARG* 2.9 29.3 + - - +
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.1 18.2 + - + +
62B VAL* 2.9 12.6 + - - +
64B THR* 1.3 80.5 - - - +
66B TYR* 1.3 62.6 + - + +
67B GLY 3.3 0.8 + - - -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 2.9 34.7 + - + +
63B LEU* 3.2 5.8 + - - +
65B GLN* 1.3 79.4 - - + +
67B GLY* 1.3 62.3 + - - +
68B ILE* 3.2 21.1 + - + +
116B GLN* 3.2 41.3 + - + -
117B VAL* 3.9 20.0 - - + -
120B ALA* 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
------------------------------------------------------------
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