Contacts of the helix formed by residues 49 - 66 (chain p) 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 p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2478 A 3.9 28.0 - - + +
10o TYR* 3.8 10.8 - - + -
13o ARG* 3.7 26.2 - - - +
45p PHE* 3.0 64.9 + - + +
48p ASN* 1.3 71.7 - - - +
50p PRO* 1.4 61.9 - - + +
51p LYS 3.0 4.3 - - - -
52p PHE* 2.8 30.1 + - + +
53p THR 3.2 7.3 + - - -
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Residues in contact with PRO 50 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K PRO* 5.8 2.0 - - + -
9L SER* 6.4 2.5 - - - -
10L TYR* 4.1 20.2 - - + -
11L SER* 5.7 0.9 - - - -
10o TYR* 3.5 35.4 - - + -
46p GLN 3.1 24.7 - - - +
47p THR 3.7 6.1 - - - +
48p ASN 3.4 2.5 - - - -
49p VAL* 1.4 96.0 - - + +
51p LYS* 1.3 65.3 + - + +
52p PHE 3.2 0.2 - - - -
53p THR* 3.7 4.7 - - - +
54p SER* 3.1 24.9 + - - -
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Residues in contact with LYS 51 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47p THR* 3.4 27.1 + - - +
48p ASN* 3.0 34.4 + - - +
50p PRO* 1.3 80.2 - - + +
52p PHE* 1.3 62.5 + - + +
54p SER* 2.9 20.0 + - - -
55p VAL* 3.4 12.8 - - - +
84p ALA* 6.2 0.4 - - - -
88p ASN* 3.8 29.7 + - - +
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Residues in contact with PHE 52 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2468 T 3.6 25.4 - - + +
2478 A 3.5 28.9 - - - +
13o ARG* 4.9 6.1 - - - +
48p ASN* 3.1 28.9 - - + -
49p VAL* 2.8 7.5 + - - +
51p LYS* 1.3 75.5 - - + +
53p THR* 1.3 66.3 + - - +
54p SER 3.2 1.3 - - - -
55p VAL* 3.1 7.0 + - - +
56p ASN* 3.0 27.8 + - - +
81p LEU* 3.5 44.6 - - + +
84p ALA* 3.6 13.2 - - + -
85p ARG* 3.5 14.4 - - - -
88p ASN* 3.4 29.2 - - - -
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Residues in contact with THR 53 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8o ARG 4.8 2.9 - - - +
9o SER* 4.3 5.2 - - - -
10o TYR* 3.5 42.1 - - + +
13o ARG* 2.8 36.5 + - - +
49p VAL 3.2 8.7 + - - -
50p PRO 3.3 8.0 + - - -
52p PHE* 1.3 78.1 - - - +
54p SER* 1.3 61.4 + - - +
56p ASN* 3.1 18.6 + - + +
57p GLU* 3.1 13.4 + - + +
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Residues in contact with SER 54 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K PRO 5.3 1.6 - - - -
54K SER* 3.3 35.5 - - - -
58K ASN* 5.3 5.4 + - - -
50p PRO 3.1 12.5 + - - -
51p LYS* 2.9 21.8 + - - -
53p THR* 1.3 77.0 - - - +
55p VAL* 1.3 62.5 + - - +
57p GLU* 3.4 10.2 + - - +
58p ASN* 3.2 28.4 + - - +
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Residues in contact with VAL 55 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51p LYS 3.4 17.7 - - - +
52p PHE* 3.2 12.6 - - - +
54p SER* 1.3 81.2 + - - +
56p ASN* 1.3 61.7 + - - +
58p ASN* 3.3 4.0 + - - +
59p VAL* 2.8 52.6 + - + +
77p GLN* 5.4 0.4 - - - +
80p GLY* 4.5 8.7 - - - +
81p LEU* 4.5 12.6 - - + +
84p ALA* 4.2 17.7 - - + -
124p ILE* 6.1 1.3 - - - -
125p ILE* 4.0 25.8 - - + -
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Residues in contact with ASN 56 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047 T 5.2 5.3 + - - +
1057 A 4.4 30.5 + - - +
13o ARG* 4.3 14.3 - - - +
52p PHE* 3.0 16.7 + - - +
53p THR* 3.1 15.7 + - + +
55p VAL* 1.3 76.0 - - - +
57p GLU* 1.3 56.9 + - - +
60p SER* 2.9 33.6 + - - -
77p GLN* 3.4 20.9 + - - +
81p LEU* 3.4 30.7 - - - +
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Residues in contact with GLU 57 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LYS* 4.2 31.9 - - - +
54K SER* 5.7 0.7 + - - -
87K LEU* 5.8 3.8 - - - +
88K ASN* 5.2 4.2 - - - +
53p THR* 3.1 12.2 + - + +
54p SER* 3.7 11.6 - - - +
55p VAL 3.2 0.2 - - - -
56p ASN* 1.3 77.6 - - - +
58p ASN* 1.3 70.1 + - - +
60p SER* 3.6 4.3 - - - -
61p ALA* 3.1 23.5 + - + +
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Residues in contact with ASN 58 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K SER* 5.5 4.8 + - - -
58K ASN* 4.2 18.6 - - - +
124K ILE* 4.3 9.8 + - - +
125K ILE* 4.2 16.1 + - - +
54p SER* 3.2 15.9 + - - +
55p VAL* 4.0 2.6 - - - +
57p GLU* 1.3 84.3 - - - +
59p VAL* 1.3 67.4 + - - +
61p ALA* 3.2 9.6 + - - +
62p VAL* 3.1 25.6 + - - +
124p ILE* 3.6 27.8 - - + +
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Residues in contact with VAL 59 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55p VAL* 2.8 42.1 + - + +
56p ASN 4.2 0.2 - - - +
58p ASN* 1.3 71.6 - - - +
60p SER* 1.3 63.8 + - - +
62p VAL* 3.1 10.0 + - - +
63p LEU* 3.0 30.7 + - + +
76p TYR 4.4 6.3 - - - +
77p GLN* 3.3 27.4 - - - +
80p GLY* 5.0 1.3 - - - -
121p VAL* 4.1 37.9 - - + +
124p ILE* 4.9 8.1 - - + -
125p ILE* 4.6 5.6 - - + -
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Residues in contact with SER 60 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 A 4.8 1.3 - - - -
1067 T 2.9 20.1 + - - -
89n ARG 4.5 3.8 + - - -
90n ILE 4.9 1.6 + - - -
56p ASN 2.9 21.7 + - - -
57p GLU* 3.6 5.4 - - - -
59p VAL* 1.3 77.1 - - - +
61p ALA* 1.3 63.0 + - - +
63p LEU* 3.1 3.6 + - - -
64p THR* 3.0 9.9 + - - -
73p ARG* 2.7 42.5 + - - +
77p GLN* 3.5 8.7 - - - +
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Residues in contact with ALA 61 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K THR 5.9 2.9 - - - +
90n ILE 5.8 0.7 - - - -
57p GLU* 3.1 15.1 + - + +
58p ASN* 3.2 12.3 + - - +
60p SER* 1.3 76.3 - - - +
62p VAL* 1.3 63.1 + - + +
64p THR* 3.2 10.0 + - - -
65p GLN* 3.1 26.2 + - + +
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Residues in contact with VAL 62 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K THR 5.0 8.5 - - - +
127K GLY* 5.1 1.3 - - - -
134K SER 5.9 0.2 - - - -
58p ASN 3.1 14.7 + - - +
59p VAL* 3.3 10.3 - - + +
61p ALA* 1.3 76.8 - - + +
63p LEU* 1.3 63.1 + - + +
65p GLN* 2.9 11.6 + - - +
66p TYR* 2.9 51.3 + - + -
117p VAL* 5.5 0.4 - - + +
120p ALA* 3.8 18.4 - - + +
121p VAL* 5.0 4.5 - - + +
124p ILE* 3.7 32.1 - - + -
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Residues in contact with LEU 63 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59p VAL* 3.0 34.5 + - + +
60p SER* 3.1 7.8 + - - +
62p VAL* 1.3 76.9 - - + +
64p THR* 1.3 61.1 + - - +
66p TYR* 3.2 3.3 + - - +
67p GLY 3.0 4.5 + - - -
68p ILE* 2.9 38.7 + - + +
73p ARG* 3.5 47.8 - - + +
76p TYR* 3.6 31.6 - - + -
77p GLN* 4.0 10.1 - - - +
117p VAL* 3.6 19.5 - - + -
121p VAL* 5.0 2.7 - - + -
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Residues in contact with THR 64 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90n ILE* 2.6 27.0 + - + +
91n GLY* 3.6 14.4 - - - +
92n SER 3.4 27.4 - - - +
93n GLY* 4.5 1.6 - - - -
94n PRO* 3.3 4.1 - - + +
95n ALA* 3.2 20.2 + - + +
60p SER 3.0 5.2 + - - -
61p ALA* 3.4 10.7 - - - -
62p VAL 3.1 0.2 - - - -
63p LEU* 1.3 76.8 - - - +
65p GLN* 1.3 65.4 + - - +
67p GLY 3.1 10.0 + - - -
73p ARG* 2.9 24.0 + - - +
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Residues in contact with GLN 65 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K SER* 4.4 17.2 + - - -
126K THR 6.0 1.1 - - - +
133K VAL* 3.9 20.2 - - - +
134K SER* 3.0 43.6 + - - +
92n SER 4.9 8.3 + - - -
93n GLY* 5.3 1.0 - - - -
94n PRO* 3.4 32.1 - - - +
61p ALA 3.1 17.5 + - - +
62p VAL* 2.9 12.4 + - - +
64p THR* 1.3 77.7 - - - +
66p TYR* 1.3 63.2 + - + +
67p GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K SER* 5.9 5.4 - - - -
94n PRO* 4.7 0.9 - - - -
62p VAL* 2.9 34.7 + - + +
63p LEU* 3.2 5.8 + - - +
65p GLN* 1.3 79.5 - - + +
67p GLY* 1.3 62.4 + - - +
68p ILE* 3.2 20.7 + - + +
116p GLN* 3.2 42.8 + - + -
117p VAL* 3.9 18.6 - - + -
120p ALA* 3.5 30.1 - - + +
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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