Contacts of the helix formed by residues 49 - 66 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318 A 3.9 28.5 - - + +
10E TYR* 3.8 10.5 - - + -
13E ARG* 3.7 26.9 - - - +
45F PHE* 3.0 63.2 + - + +
48F ASN* 1.3 71.0 - - - +
50F PRO* 1.4 61.3 - - + +
51F LYS 3.0 4.3 - - - -
52F PHE* 2.8 30.5 + - + +
53F THR 3.2 6.8 + - - -
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Residues in contact with PRO 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E TYR* 3.5 37.7 - - + -
46F GLN 3.1 25.4 - - - +
47F THR 3.7 6.1 - - - +
48F ASN 3.4 2.5 - - - -
49F VAL* 1.4 97.1 - - + +
51F LYS* 1.3 64.5 + - + +
52F PHE 3.2 0.2 - - - -
53F THR* 3.7 4.5 - - - +
54F SER* 3.1 24.9 + - - -
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Residues in contact with LYS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F THR* 3.4 27.7 + - - +
48F ASN* 3.0 34.1 + - - +
49F VAL 3.0 0.2 - - - -
50F PRO* 1.3 81.3 - - + +
52F PHE* 1.3 63.4 + - + +
54F SER* 2.9 19.5 + - - -
55F VAL* 3.4 12.5 - - - +
84F ALA* 6.2 0.2 - - - -
88F ASN* 3.8 29.7 + - - +
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Residues in contact with PHE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308 T 3.6 24.0 - - + -
318 A 3.5 29.2 - - - +
13E ARG* 4.6 6.1 - - - +
48F ASN* 3.1 29.4 - - + -
49F VAL* 2.8 6.9 + - - +
51F LYS* 1.3 77.5 - - + +
53F THR* 1.3 66.6 + - - +
54F SER 3.2 0.4 - - - -
55F VAL* 3.1 7.7 + - - +
56F ASN* 3.0 26.9 + - - +
81F LEU* 3.5 45.5 - - + +
84F ALA* 3.6 12.6 - - + -
85F ARG* 3.5 13.7 - - - -
88F ASN* 3.4 28.9 - - - -
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Residues in contact with THR 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG 4.8 3.4 - - - +
9E SER* 4.3 5.4 - - - -
10E TYR* 3.5 42.5 - - + +
13E ARG* 2.8 36.9 + - - +
49F VAL 3.2 7.8 + - - -
50F PRO* 3.3 8.3 + - - -
52F PHE* 1.3 78.8 - - - +
54F SER* 1.3 60.5 + - - +
56F ASN* 3.1 18.2 + - + +
57F GLU* 3.1 12.6 + - + +
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PRO 3.1 12.3 + - - -
51F LYS* 2.9 22.2 + - - -
53F THR* 1.3 76.6 - - - +
55F VAL* 1.3 62.7 + - - +
57F GLU* 3.4 10.5 + - - +
58F ASN* 3.2 29.4 + - - +
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Residues in contact with VAL 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F LYS 3.4 17.3 - - - +
52F PHE* 3.1 13.4 + - - +
54F SER* 1.3 82.3 + - - +
56F ASN* 1.3 59.8 + - - +
58F ASN* 3.3 4.3 + - - +
59F VAL* 2.8 53.1 + - + +
77F GLN* 5.4 0.4 - - - +
80F GLY* 4.5 8.3 - - - +
81F LEU* 4.5 13.5 - - + +
84F ALA* 4.2 17.5 - - + -
124F ILE* 6.1 1.1 - - - -
125F ILE* 4.0 24.9 - - + -
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Residues in contact with ASN 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3207 T 5.2 4.8 + - - +
3217 A 4.4 31.6 + - - +
13E ARG* 4.3 14.8 - - - +
52F PHE 3.0 17.1 + - - -
53F THR* 3.4 14.7 - - + +
55F VAL* 1.3 76.9 - - - +
57F GLU* 1.3 57.0 + - - +
60F SER* 2.9 33.3 + - - -
77F GLN* 3.4 20.6 + - - +
81F LEU* 3.4 30.2 - - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 3.1 13.0 + - + +
54F SER* 3.7 11.6 - - - +
55F VAL 3.2 0.2 - - - -
56F ASN* 1.3 77.9 - - - +
58F ASN* 1.3 70.2 + - - +
60F SER* 3.6 3.5 - - - -
61F ALA* 3.1 22.7 + - + +
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Residues in contact with ASN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F SER* 3.2 17.3 + - - +
55F VAL* 4.0 2.2 - - - +
57F GLU* 1.3 84.9 - - - +
59F VAL* 1.3 66.8 + - - +
61F ALA* 3.2 9.7 + - - +
62F VAL* 3.1 26.5 + - - +
124F ILE* 3.6 28.4 - - + +
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Residues in contact with VAL 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F VAL* 2.8 42.0 + - + +
58F ASN* 1.3 71.6 - - - +
60F SER* 1.3 63.7 + - - +
62F VAL* 3.1 9.5 + - - +
63F LEU* 3.0 30.7 + - + +
76F TYR 4.4 7.0 - - - +
77F GLN* 3.3 28.3 - - - +
80F GLY* 5.0 1.8 - - - -
121F VAL* 4.1 37.9 - - + +
124F ILE* 4.9 7.6 - - + -
125F ILE* 4.6 6.3 - - + -
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3217 A 4.8 1.3 - - - -
3227 T 2.9 19.9 + - - -
89D ARG 4.5 4.0 + - - -
90D ILE 4.9 2.0 + - - -
56F ASN 2.9 21.1 + - - -
57F GLU* 3.6 4.7 - - - -
59F VAL* 1.3 77.7 - - - +
61F ALA* 1.3 63.0 + - - +
63F LEU* 3.1 3.2 + - - -
64F THR* 3.0 9.9 + - - -
73F ARG* 2.7 41.8 + - - +
77F GLN* 3.5 8.9 - - - +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ILE 5.8 0.7 - - - -
57F GLU* 3.1 14.9 + - + +
58F ASN* 3.4 13.0 - - - +
60F SER* 1.3 76.7 - - - +
62F VAL* 1.3 62.4 + - + +
64F THR* 3.2 10.2 + - - -
65F GLN* 3.1 26.1 + - + +
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F ASN 3.1 14.5 + - - +
59F VAL* 3.1 10.1 + - + +
61F ALA* 1.3 77.2 - - + +
63F LEU* 1.3 63.6 + - + +
65F GLN* 2.9 11.9 + - + +
66F TYR* 2.9 50.1 + - + -
117F VAL* 5.5 0.7 - - + +
120F ALA* 3.8 18.4 - - + -
121F VAL* 5.0 4.5 - - + +
124F ILE* 3.7 32.5 - - + -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F VAL* 3.0 33.2 + - + +
60F SER* 3.1 7.8 + - - +
62F VAL* 1.3 77.4 - - + +
64F THR* 1.3 61.0 + - - +
66F TYR* 3.2 3.5 + - - +
67F GLY 3.0 4.7 + - - -
68F ILE* 2.9 38.4 + - + +
73F ARG* 3.5 48.5 - - + +
76F TYR* 3.6 32.1 - - + -
77F GLN* 4.0 10.1 - - - +
117F VAL* 3.6 19.5 - - + -
121F VAL* 5.0 2.7 - - + -
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Residues in contact with THR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 2.6 27.5 + - + +
91D GLY* 3.6 14.1 - - - +
92D SER 3.4 27.4 - - - +
93D GLY* 4.5 1.8 - - - -
94D PRO* 3.3 4.1 - - + +
95D ALA* 3.2 19.6 + - + +
60F SER 3.0 4.9 + - - -
61F ALA* 3.4 11.2 - - - -
62F VAL 3.1 0.2 - - - -
63F LEU* 1.3 77.0 - - - +
65F GLN* 1.3 63.8 + - - +
67F GLY 3.1 10.2 + - - -
73F ARG* 2.9 23.3 + - - +
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Residues in contact with GLN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER 4.9 7.7 + - - -
93D GLY* 5.3 0.8 - - - -
94D PRO* 3.4 31.9 - - - +
61F ALA 3.1 17.5 + - - +
62F VAL* 2.9 12.6 + - + +
64F THR* 1.3 77.0 - - - +
66F TYR* 1.3 63.6 + - + +
67F GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PRO* 4.7 0.9 - - - -
62F VAL* 2.9 36.2 + - + +
63F LEU* 3.2 6.0 + - - +
65F GLN* 1.3 79.3 - - + +
67F GLY* 1.3 61.7 + - - +
68F ILE* 3.2 20.8 + - + +
116F GLN* 3.2 41.3 + - + -
117F VAL* 3.9 19.5 - - + -
120F ALA* 3.5 30.7 - - + +
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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