Contacts of the helix formed by residues 49 - 66 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678 A 3.9 28.5 - - + +
10K TYR* 3.8 10.3 - - + -
13K ARG* 3.7 27.1 - - - +
45L PHE* 3.0 63.6 + - + +
48L ASN* 1.3 71.7 - - - +
50L PRO* 1.4 61.9 - - + +
51L LYS 3.0 4.0 - - - -
52L PHE* 2.8 31.4 + - + +
53L THR* 3.2 6.9 + - - -
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Residues in contact with PRO 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K TYR* 3.5 38.8 - - + -
46L GLN 3.1 26.0 - - - +
47L THR 3.7 5.8 - - - +
48L ASN 3.4 2.5 - - - -
49L VAL* 1.4 96.4 - - + +
51L LYS* 1.3 65.6 + - + +
53L THR* 3.7 5.3 - - - +
54L SER* 3.1 25.1 + - - -
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Residues in contact with LYS 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L THR* 3.4 27.7 + - - +
48L ASN* 3.0 34.1 + - - +
50L PRO* 1.3 80.1 - - + +
52L PHE* 1.3 63.9 + - + +
54L SER* 2.9 20.6 + - - -
55L VAL* 3.4 11.6 - - - +
84L ALA* 5.7 0.4 - - - +
88L ASN* 3.8 29.7 + - - +
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Residues in contact with PHE 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668 T 3.6 24.9 - - + +
678 A 3.5 29.4 - - - +
13K ARG* 4.6 5.6 - - - +
48L ASN* 3.1 28.5 - - + -
49L VAL* 2.8 7.6 + - + +
51L LYS* 1.3 76.9 - - + +
53L THR* 1.3 66.8 + - - +
54L SER 3.2 1.3 - - - -
55L VAL* 3.1 7.6 + - - +
56L ASN* 3.0 26.9 + - - +
81L LEU* 3.5 44.8 - - + +
84L ALA* 3.6 13.5 - - + -
85L ARG* 3.5 13.5 - - - -
88L ASN* 3.4 28.7 - - - -
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Residues in contact with THR 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ARG 4.8 2.7 - - - +
9K SER* 4.3 5.8 - - - -
10K TYR* 3.5 42.1 - - + +
13K ARG* 2.8 37.9 + - - +
49L VAL 3.2 8.0 + - - -
50L PRO 3.3 7.8 + - - -
52L PHE* 1.3 78.2 - - - +
54L SER* 1.3 62.8 + - - +
56L ASN* 3.1 18.9 + - + +
57L GLU* 3.1 12.3 + - + +
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Residues in contact with SER 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L PRO 3.1 12.5 + - - -
51L LYS* 2.9 21.5 + - - -
53L THR* 1.3 77.1 - - - +
55L VAL* 1.3 63.9 + - - +
57L GLU* 3.4 10.4 + - - +
58L ASN* 3.2 29.0 + - - +
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L LYS 3.4 17.3 - - - +
52L PHE* 3.1 14.0 + - - +
54L SER* 1.3 82.9 + - - +
56L ASN* 1.3 60.2 + - - +
58L ASN* 3.3 4.1 + - - +
59L VAL* 2.8 52.9 + - + +
77L GLN* 5.4 0.7 - - - +
80L GLY 4.5 8.1 - - - +
81L LEU* 4.5 12.6 - - + -
84L ALA* 4.2 18.2 - - + -
124L ILE* 6.1 1.3 - - - -
125L ILE* 4.0 26.0 - - + -
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Residues in contact with ASN 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2847 T 5.2 5.1 + - - +
2857 A 4.4 30.5 + - - +
13K ARG* 4.3 13.3 - - - +
52L PHE* 3.0 17.7 + - - +
53L THR* 3.4 14.6 - - + +
55L VAL* 1.3 77.0 - - - +
57L GLU* 1.3 57.1 + - - +
60L SER* 2.9 34.0 + - - -
77L GLN* 3.4 20.1 + - - +
81L LEU* 3.4 30.4 - - - +
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Residues in contact with GLU 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L THR* 3.1 12.0 + - + +
54L SER* 3.7 11.4 - - - +
55L VAL 3.2 0.4 - - - -
56L ASN* 1.3 78.3 - - - +
58L ASN* 1.3 70.6 + - - +
60L SER* 3.6 3.3 - - - -
61L ALA* 3.1 22.9 + - + +
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Residues in contact with ASN 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L SER* 3.2 18.7 + - - +
55L VAL* 4.0 1.5 - - - +
57L GLU* 1.3 85.8 - - - +
59L VAL* 1.3 66.0 + - - +
61L ALA* 3.2 9.1 + - - +
62L VAL* 3.1 26.7 + - - +
124L ILE* 3.6 29.1 - - + +
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Residues in contact with VAL 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L VAL* 2.8 41.7 + - + +
58L ASN* 1.3 72.5 - - - +
60L SER* 1.3 62.8 + - - +
62L VAL* 3.1 9.5 + - - +
63L LEU* 3.0 30.7 + - + +
76L TYR 4.4 6.7 - - - +
77L GLN* 3.3 27.1 - - - +
80L GLY* 5.0 1.3 - - - -
121L VAL* 4.1 37.7 - - + +
124L ILE* 4.9 8.3 - - + -
125L ILE* 4.6 6.1 - - + -
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Residues in contact with SER 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2857 A 4.8 0.9 - - - -
2867 T 2.9 20.2 + - - -
89J ARG 4.5 4.2 + - - -
90J ILE 4.9 2.5 + - - -
56L ASN 2.9 20.7 + - - -
57L GLU* 3.6 4.7 - - - -
59L VAL* 1.3 77.3 - - - +
61L ALA* 1.3 61.9 + - - +
63L LEU* 3.1 3.5 + - - -
64L THR* 3.0 10.6 + - - -
73L ARG* 2.7 41.3 + - - +
77L GLN* 3.5 8.6 - - - +
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Residues in contact with ALA 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J ILE 5.8 0.7 - - - -
57L GLU* 3.1 15.8 + - + +
58L ASN* 3.4 12.3 - - - +
60L SER* 1.3 75.8 - - - +
62L VAL* 1.3 63.0 + - + +
64L THR* 3.2 10.4 + - - -
65L GLN* 3.1 26.0 + - + +
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Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ASN 3.1 14.4 + - - +
59L VAL* 3.3 9.4 - - + +
61L ALA* 1.3 76.2 - - + +
63L LEU* 1.3 63.8 + - + +
65L GLN* 2.9 11.7 + - + +
66L TYR* 2.9 50.3 + - + -
117L VAL* 5.5 0.7 - - + +
120L ALA* 3.8 18.2 - - + -
121L VAL* 5.0 4.3 - - + +
124L ILE* 3.7 33.0 - - + -
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Residues in contact with LEU 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L VAL* 3.0 33.8 + - + +
60L SER* 3.1 7.8 + - - +
62L VAL* 1.3 76.3 - - + +
64L THR* 1.3 61.4 + - - +
66L TYR* 3.2 3.0 + - - +
67L GLY 3.0 4.3 + - - -
68L ILE* 2.9 39.2 + - + -
73L ARG* 3.5 48.0 - - + +
76L TYR* 3.6 32.1 - - + -
77L GLN* 4.0 9.9 - - - +
117L VAL* 3.6 18.8 - - + -
121L VAL* 5.0 3.1 - - + -
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Residues in contact with THR 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J ILE* 2.6 28.6 + - + +
91J GLY* 3.6 13.9 - - - +
92J SER 3.4 27.8 - - - +
93J GLY* 4.5 1.3 - - - -
94J PRO* 3.3 4.3 - - + +
95J ALA* 3.2 19.6 + - + +
60L SER 3.0 5.8 + - - -
61L ALA* 3.4 10.7 - - - -
63L LEU* 1.3 77.4 - - - +
65L GLN* 1.3 64.8 + - - +
67L GLY 3.1 10.6 + - - -
73L ARG* 2.9 21.9 + - - +
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Residues in contact with GLN 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J SER 4.9 7.9 + - - -
93J GLY* 5.3 1.4 - - - -
94J PRO* 3.4 31.6 - - - +
61L ALA* 3.1 16.9 + - + +
62L VAL* 2.9 12.4 + - + +
64L THR* 1.3 77.7 - - - +
66L TYR* 1.3 64.1 + - + +
67L GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J PRO* 4.7 0.7 - - - -
62L VAL* 2.9 34.1 + - + +
63L LEU* 3.2 5.6 + - - +
65L GLN* 1.3 79.9 - - + +
67L GLY* 1.3 62.0 + - - +
68L ILE* 3.2 20.9 + - + +
116L GLN* 3.2 41.7 + - + -
117L VAL* 3.9 18.4 - - + -
120L 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