Contacts of the helix formed by residues 49 - 66 (chain t) 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 t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2718 A 3.9 28.5 - - + +
10s TYR* 3.8 10.1 - - + -
13s ARG* 3.7 26.7 - - - +
45t PHE* 3.0 65.0 + - + +
48t ASN* 1.3 71.5 - - - +
50t PRO* 1.4 61.0 - - + +
51t LYS 3.0 4.0 - - - -
52t PHE* 2.8 30.9 + - - +
53t THR 3.2 7.1 + - - -
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Residues in contact with PRO 50 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PRO* 5.8 1.8 - - + -
9P SER* 6.4 2.9 - - - -
10P TYR* 4.1 20.6 - - + -
11P SER* 5.7 0.9 - - - -
10s TYR* 3.5 35.4 - - + -
46t GLN 3.1 24.5 - - - +
47t THR 3.7 6.3 - - - +
48t ASN 3.4 2.5 - - - -
49t VAL* 1.4 96.9 - - + +
51t LYS* 1.3 65.7 + - + +
52t PHE 3.2 0.2 - - - -
53t THR* 3.7 4.9 - - - +
54t SER* 3.1 24.3 + - - -
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Residues in contact with LYS 51 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47t THR* 3.4 27.9 + - - +
48t ASN* 3.0 34.7 + - - +
50t PRO* 1.3 80.2 - - + +
52t PHE* 1.3 64.0 + - + +
54t SER* 2.9 20.4 + - - -
55t VAL* 3.4 12.3 - - - +
84t ALA* 5.7 0.4 - - - +
88t ASN* 3.8 29.2 + - - +
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Residues in contact with PHE 52 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2708 T 3.6 24.9 - - + +
2718 A 3.5 29.4 - - - +
13s ARG* 4.6 6.1 - - - +
48t ASN* 3.1 29.2 - - + -
49t VAL* 2.8 7.3 + - - +
51t LYS* 1.3 75.7 - - + +
53t THR* 1.3 66.9 + - - +
54t SER 3.2 1.6 - - - -
55t VAL* 3.1 8.2 + - - +
56t ASN* 3.0 27.7 + - - +
81t LEU* 3.5 44.6 - - + -
84t ALA* 3.6 13.0 - - + -
85t ARG* 3.5 13.9 - - - -
88t ASN* 3.4 28.7 - - - -
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Residues in contact with THR 53 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8s ARG 4.8 2.9 - - - +
9s SER* 4.3 5.2 - - - -
10s TYR* 3.5 42.5 - - + +
13s ARG* 2.8 36.7 + - - +
49t VAL 3.2 8.2 + - - -
50t PRO* 3.3 7.8 + - - -
52t PHE* 1.3 77.4 - - - +
54t SER* 1.3 61.7 + - - +
56t ASN* 3.1 18.9 + - + +
57t GLU* 3.1 13.5 + - + +
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Residues in contact with SER 54 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PRO 5.3 1.6 - - - -
54O SER* 3.3 35.7 - - - -
58O ASN* 5.3 5.6 + - - -
50t PRO 3.1 12.4 + - - -
51t LYS* 2.9 21.8 + - - -
53t THR* 1.3 76.6 - - - +
55t VAL* 1.3 62.9 + - - +
57t GLU* 3.4 9.8 + - - +
58t ASN* 3.2 27.5 + - - +
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Residues in contact with VAL 55 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51t LYS 3.4 17.3 - - - +
52t PHE* 3.1 12.1 + - - +
54t SER* 1.3 81.9 + - - +
56t ASN* 1.3 61.8 + - - +
58t ASN* 3.3 3.9 + - - +
59t VAL* 2.8 53.1 + - + +
77t GLN* 5.4 0.4 - - - +
80t GLY 4.5 8.7 - - - +
81t LEU* 4.5 12.8 - - + -
84t ALA* 4.2 18.4 - - + -
124t ILE* 6.1 1.1 - - - -
125t ILE* 4.0 25.4 - - + -
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Residues in contact with ASN 56 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807 T 5.2 5.1 + - - +
817 A 4.4 30.8 + - - -
13s ARG* 4.3 14.1 - - - +
52t PHE* 3.0 15.5 + - - +
53t THR* 3.1 15.5 + - + +
55t VAL* 1.3 77.5 - - - +
57t GLU* 1.3 55.8 + - - +
60t SER* 2.9 33.1 + - - -
77t GLN* 3.4 21.6 + - - +
81t LEU* 3.4 30.5 - - - +
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Residues in contact with GLU 57 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O LYS* 4.2 31.8 - - - +
54O SER* 5.7 0.7 + - - -
87O LEU* 5.8 3.6 - - - +
88O ASN* 5.2 4.2 - - - +
53t THR* 3.1 12.4 + - + +
54t SER* 3.7 11.7 - - - +
55t VAL 3.2 0.2 - - - -
56t ASN* 1.3 77.2 - - - +
58t ASN* 1.3 71.0 + - - +
60t SER* 3.6 4.3 - - - -
61t ALA* 3.1 22.8 + - + +
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Residues in contact with ASN 58 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O SER* 5.5 5.1 + - - -
58O ASN* 4.2 18.0 - - - +
124O ILE* 4.3 9.8 + - - +
125O ILE* 4.2 17.0 + - - +
54t SER* 3.2 15.5 + - - +
55t VAL* 4.0 2.4 - - - +
57t GLU* 1.3 85.2 - - - +
59t VAL* 1.3 67.2 + - - +
61t ALA* 3.2 9.1 + - - +
62t VAL* 3.1 25.8 + - - +
124t ILE* 3.6 28.2 - - + +
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Residues in contact with VAL 59 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55t VAL* 2.8 41.5 + - + +
58t ASN* 1.3 71.5 - - - +
60t SER* 1.3 64.1 + - - +
62t VAL* 3.1 9.3 + - - +
63t LEU* 3.0 30.8 + - + +
76t TYR 4.4 6.7 - - - +
77t GLN* 3.3 27.4 - - - +
80t GLY* 5.0 0.9 - - - -
121t VAL* 4.1 37.7 - - + +
124t ILE* 4.9 9.4 - - + -
125t ILE* 4.6 6.5 - - + -
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Residues in contact with SER 60 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817 A 4.8 1.3 - - - -
827 T 2.9 20.3 + - - -
89r ARG 4.5 4.5 + - - -
90r ILE 4.9 1.6 + - - -
56t ASN 2.9 21.8 + - - -
57t GLU* 3.6 4.9 - - - -
59t VAL* 1.3 76.3 - - - +
61t ALA* 1.3 63.2 + - - +
63t LEU* 3.1 3.5 + - - -
64t THR* 3.0 9.6 + - - -
73t ARG* 2.7 44.0 + - - +
77t GLN* 3.5 8.4 - - - +
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Residues in contact with ALA 61 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O THR 5.9 2.9 - - - +
90r ILE 5.8 0.7 - - - -
57t GLU* 3.1 14.9 + - + +
58t ASN* 3.2 13.0 + - - +
60t SER* 1.3 75.8 - - - +
62t VAL* 1.3 63.0 + - + +
64t THR* 3.2 10.0 + - - +
65t GLN* 3.1 25.8 + - + +
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Residues in contact with VAL 62 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O THR 5.0 8.5 - - - +
127O GLY* 5.1 1.1 - - - -
58t ASN 3.1 14.3 + - - +
59t VAL* 3.3 9.4 - - + +
61t ALA* 1.3 78.3 - - + +
63t LEU* 1.3 63.0 + - + +
65t GLN* 2.9 11.4 + - + +
66t TYR* 2.9 50.9 + - + -
117t VAL* 5.5 0.7 - - + +
120t ALA* 3.8 18.4 - - + +
121t VAL* 5.0 3.8 - - + +
124t ILE* 3.7 33.0 - - + -
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Residues in contact with LEU 63 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59t VAL* 3.0 33.2 + - + +
60t SER* 3.1 8.0 + - - +
62t VAL* 1.3 76.8 - - + +
64t THR* 1.3 60.8 + - - +
66t TYR* 3.2 2.9 + - - +
67t GLY 3.0 4.5 + - - -
68t ILE* 2.9 39.0 + - + +
73t ARG* 3.5 47.3 - - + +
76t TYR* 3.6 31.6 - - + -
77t GLN* 4.0 10.1 - - - +
117t VAL* 3.6 19.3 - - + -
121t VAL* 5.0 2.9 - - + -
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Residues in contact with THR 64 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90r ILE* 2.6 28.5 + - + +
91r GLY 3.6 13.7 - - - +
92r SER 3.4 27.1 - - - +
93r GLY* 4.5 1.6 - - - -
94r PRO* 3.3 3.9 - - + +
95r ALA* 3.2 19.9 + - + +
60t SER 3.0 5.6 + - - -
61t ALA* 3.4 10.5 - - - -
63t LEU* 1.3 77.4 - - - +
65t GLN* 1.3 63.4 + - - +
67t GLY 3.1 10.2 + - - -
73t ARG* 2.9 22.5 + - - +
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Residues in contact with GLN 65 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O SER* 4.4 17.2 + - - -
126O THR 6.0 1.1 - - - +
133O VAL* 3.9 20.1 - - - +
134O SER* 3.0 43.8 + - - +
92r SER 4.9 8.5 + - - -
93r GLY* 5.3 1.2 - - - -
94r PRO* 3.4 30.1 - - - +
61t ALA 3.1 16.7 + - - +
62t VAL* 2.9 12.4 + - - +
64t THR* 1.3 77.7 - - - +
66t TYR* 1.3 62.9 + - + +
67t GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O SER* 5.9 5.2 - - - -
94r PRO* 4.7 0.7 - - - -
62t VAL* 2.9 33.3 + - + +
63t LEU* 3.2 6.0 + - - +
65t GLN* 1.3 81.4 - - + +
67t GLY* 1.3 61.8 + - - +
68t ILE* 3.2 20.6 + - + +
116t GLN* 3.2 42.1 + - + -
117t VAL* 3.9 20.0 - - + -
120t ALA* 3.5 30.4 - - + +
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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