Contacts of the helix formed by residues 49 - 66 (chain v) 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 v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2838 A 3.9 28.7 - - + +
10u TYR* 3.8 10.3 - - + -
13u ARG* 3.7 26.9 - - - +
45v PHE* 3.0 63.1 + - + +
48v ASN* 1.3 70.2 - - - +
50v PRO* 1.3 62.8 - - + +
51v LYS 3.0 4.0 - - - -
52v PHE* 2.8 30.9 + - + +
53v THR 3.2 6.9 + - - -
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Residues in contact with PRO 50 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q PRO* 5.8 1.6 - - + -
9R SER* 6.4 2.2 - - - -
10R TYR* 4.1 21.1 - - + -
11R SER* 5.7 0.9 - - - -
10u TYR* 3.5 35.6 - - + -
46v GLN 3.1 24.9 - - - +
47v THR 3.7 6.1 - - - +
48v ASN 3.4 2.7 - - - -
49v VAL* 1.3 96.2 - - + +
51v LYS* 1.3 65.6 + - + +
53v THR* 3.7 4.9 - - - +
54v SER* 3.1 24.4 + - - -
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Residues in contact with LYS 51 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47v THR* 3.4 27.7 + - - +
48v ASN* 3.0 34.8 + - - +
49v VAL 2.9 0.4 + - - -
50v PRO* 1.3 80.6 - - + +
52v PHE* 1.3 63.2 + - + +
54v SER* 2.9 19.4 + - - -
55v VAL* 3.4 12.1 - - - +
84v ALA* 5.7 0.6 - - - +
88v ASN* 3.8 29.2 + - - +
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Residues in contact with PHE 52 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2828 T 3.6 24.2 - - + -
2838 A 3.5 28.5 - - - +
13u ARG* 4.9 5.8 - - - +
48v ASN* 3.1 28.9 - - + -
49v VAL* 2.8 7.1 + - - +
51v LYS* 1.3 79.0 - - + +
53v THR* 1.3 65.5 + - - +
54v SER 3.2 0.4 - - - -
55v VAL* 3.1 7.6 + - - +
56v ASN* 3.0 26.9 + - - +
81v LEU* 3.5 44.9 - - + -
84v ALA* 3.6 12.8 - - + -
85v ARG* 3.5 14.1 - - - -
88v ASN* 3.4 29.4 - - - -
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Residues in contact with THR 53 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8u ARG 4.8 2.7 - - - +
9u SER* 4.3 5.6 - - - -
10u TYR* 3.5 41.6 - - + +
13u ARG* 2.8 36.8 + - - +
49v VAL 3.2 8.4 + - - -
50v PRO 3.3 8.0 + - - -
52v PHE* 1.3 78.6 - - - +
54v SER* 1.3 62.4 + - - +
56v ASN* 3.1 17.9 + - + +
57v GLU* 3.1 13.2 + - + +
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Residues in contact with SER 54 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q PRO 5.3 1.3 - - - -
54Q SER* 3.3 35.3 - - - -
58Q ASN* 5.3 5.0 + - - -
50v PRO 3.1 12.7 + - - -
51v LYS* 2.9 21.7 + - - -
53v THR* 1.3 76.9 - - - +
55v VAL* 1.3 63.3 + - - +
57v GLU* 3.4 9.8 + - - +
58v ASN* 3.2 28.4 + - - +
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Residues in contact with VAL 55 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51v LYS 3.4 17.5 - - - +
52v PHE* 3.1 13.4 + - - +
54v SER* 1.3 83.7 + - - +
56v ASN* 1.3 59.7 - - - +
58v ASN* 3.3 3.9 + - - +
59v VAL* 2.8 53.1 + - + +
77v GLN* 5.4 0.7 - - - +
80v GLY 4.5 8.3 - - - +
81v LEU* 4.5 12.1 - - + -
84v ALA* 4.2 18.2 - - + -
124v ILE* 6.1 1.3 - - - -
125v ILE* 4.0 25.1 - - + -
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Residues in contact with ASN 56 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687 T 5.2 5.5 + - - +
697 A 4.4 30.8 + - - -
13u ARG* 4.3 14.3 - - - +
52v PHE 3.0 16.1 + - - -
53v THR* 3.1 16.1 + - + +
55v VAL* 1.3 76.9 - - - +
57v GLU* 1.3 57.3 + - - +
60v SER* 2.9 33.6 + - - -
77v GLN* 3.4 19.5 + - - +
81v LEU* 3.4 31.1 - - - +
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Residues in contact with GLU 57 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q LYS* 4.2 31.5 - - - +
54Q SER* 5.7 0.5 + - - -
87Q LEU* 5.8 3.5 - - - +
88Q ASN* 5.2 4.5 - - - +
53v THR* 3.1 12.2 + - + +
54v SER* 3.7 11.6 - - - +
55v VAL 3.2 0.4 - - - -
56v ASN* 1.3 77.8 - - - +
58v ASN* 1.3 70.4 + - - +
60v SER* 3.6 4.1 - - - -
61v ALA* 3.0 22.8 + - + +
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Residues in contact with ASN 58 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q SER* 5.5 4.8 + - - -
55Q VAL* 6.4 0.2 - - - +
58Q ASN* 4.2 18.4 - - - +
124Q ILE* 4.3 9.6 + - - +
125Q ILE* 4.2 16.8 + - - +
54v SER* 3.2 16.7 + - - +
55v VAL* 4.0 2.2 - - - +
57v GLU* 1.3 84.8 - - - +
59v VAL* 1.3 67.1 + - - +
61v ALA* 3.2 8.9 + - - +
62v VAL* 3.1 25.9 + - - +
124v ILE* 3.6 28.0 - - + +
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Residues in contact with VAL 59 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55v VAL* 2.8 42.3 + - + +
58v ASN* 1.3 70.8 - - - +
60v SER* 1.3 63.7 + - - +
62v VAL* 3.1 10.3 + - - +
63v LEU* 3.0 30.6 + - + +
76v TYR 4.4 6.5 - - - +
77v GLN* 3.3 27.6 - - - +
80v GLY* 5.0 1.8 - - - -
121v VAL* 4.1 37.9 - - + +
124v ILE* 4.9 8.3 - - + -
125v ILE* 4.6 6.3 - - + -
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Residues in contact with SER 60 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 A 4.8 1.1 - - - -
707 T 2.9 20.3 + - - -
89t ARG 4.5 4.0 + - - -
90t ILE 4.9 1.7 + - - -
56v ASN 2.9 21.6 + - - -
57v GLU* 3.6 4.9 - - - -
59v VAL* 1.3 77.1 - - - +
61v ALA* 1.3 62.1 + - - +
63v LEU* 3.1 3.5 + - - -
64v THR* 3.0 10.6 + - - -
73v ARG* 2.7 42.1 + - - +
77v GLN* 3.5 7.8 - - - +
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Residues in contact with ALA 61 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Q THR 5.9 2.5 - - - +
90t ILE 5.8 0.7 - - - -
57v GLU* 3.0 15.1 + - + +
58v ASN* 3.2 12.5 + - - +
60v SER* 1.3 76.3 - - - +
62v VAL* 1.3 62.4 + - + +
64v THR* 3.2 10.1 + - - -
65v GLN* 3.1 25.7 + - + +
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Residues in contact with VAL 62 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q THR 5.0 8.5 - - - +
127Q GLY* 5.1 1.6 - - - -
58v ASN 3.1 14.8 + - - +
59v VAL* 3.1 10.0 + - + +
61v ALA* 1.3 76.4 - - + +
63v LEU* 1.3 64.5 + - + +
65v GLN* 2.9 11.2 + - - +
66v TYR* 2.9 50.5 + - + -
117v VAL* 5.5 0.7 - - + +
120v ALA* 3.8 18.2 - - + +
121v VAL* 5.0 4.0 - - + +
124v ILE* 3.7 32.1 - - + -
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Residues in contact with LEU 63 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59v VAL* 3.0 33.7 + - + +
60v SER* 3.4 7.2 - - - +
62v VAL* 1.3 77.4 - - + +
64v THR* 1.3 61.5 + - - +
66v TYR* 3.2 2.6 + - - +
67v GLY 3.0 4.3 + - - -
68v ILE* 2.9 39.8 + - + -
73v ARG* 3.5 47.1 - - + +
76v TYR* 3.6 31.6 - - + -
77v GLN* 4.0 10.3 - - - +
117v VAL* 3.6 19.3 - - + -
121v VAL* 5.0 3.1 - - + -
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Residues in contact with THR 64 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90t ILE* 2.6 28.8 + - + +
91t GLY* 3.6 13.5 - - - +
92t SER 3.4 27.8 - - - +
93t GLY* 4.5 1.6 - - - -
94t PRO* 3.3 4.3 - - + +
95t ALA* 3.2 19.5 + - + +
60v SER 3.0 5.2 + - - -
61v ALA* 3.4 11.8 - - - -
63v LEU* 1.3 76.6 - - - +
65v GLN* 1.3 64.0 + - - +
67v GLY 3.1 10.2 + - - -
73v ARG* 2.9 23.3 + - - +
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Residues in contact with GLN 65 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q SER* 4.4 17.0 + - - -
126Q THR 6.0 1.1 - - - +
133Q VAL* 3.9 21.5 - - - +
134Q SER* 3.0 43.2 + - - +
92t SER 4.9 7.9 + - - -
93t GLY* 5.3 0.8 - - - -
94t PRO* 3.4 31.4 - - - +
61v ALA* 3.1 17.4 + - + +
62v VAL* 2.9 12.4 + - - +
64v THR* 1.3 77.4 - - - +
66v TYR* 1.3 63.5 + - + +
67v GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q SER* 5.9 4.7 - - - -
94t PRO* 4.7 0.7 - - - -
62v VAL* 2.9 34.9 + - + +
63v LEU* 3.2 5.6 + - - +
65v GLN* 1.3 79.9 - - + +
67v GLY* 1.3 61.9 + - - +
68v ILE* 3.4 20.6 + - + +
116v GLN* 3.2 41.2 + - + -
117v VAL* 3.9 19.7 - - + -
120v ALA* 3.5 30.3 - - + +
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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