Contacts of the helix formed by residues 8 - 30 (chain I) in PDB entry 1YV0
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 ARG 8 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4I GLU* 4.3 7.2 + - - -
5I LYS* 3.2 43.6 + - - +
6I LYS 3.1 3.1 + - - -
7I ARG* 1.3 82.6 - - - +
9I ALA* 1.3 59.6 + - - +
10I ALA 3.6 0.4 - - - -
11I THR* 4.4 3.2 + - - -
12I ALA* 3.4 20.5 + - - +
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Residues in contact with ALA 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I LYS 3.7 8.5 + - - +
8I ARG* 1.3 79.1 - - - +
10I ALA* 1.3 59.2 + - - +
11I THR 3.2 2.2 - - - -
12I ALA* 3.4 8.8 - - + +
13I ARG* 3.0 34.3 + - + +
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Residues in contact with ALA 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ASP* 5.5 2.8 - - - +
6I LYS 4.4 2.3 + - - +
7I ARG* 4.3 22.0 - - + -
8I ARG 3.6 1.2 - - - +
9I ALA* 1.3 77.8 - - - +
11I THR* 1.3 57.1 + - - +
13I ARG* 3.8 6.0 - - - +
14I ARG* 3.2 41.4 + - - +
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Residues in contact with THR 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I ARG* 3.5 23.2 + - - +
8I ARG* 4.6 3.3 + - - -
10I ALA* 1.3 72.9 - - - +
12I ALA* 1.3 60.5 + - - +
13I ARG 2.9 2.2 - - - -
14I ARG* 2.8 33.2 + - - +
15I GLN* 2.4 58.4 + - + +
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ARG 3.4 18.4 + - - +
9I ALA* 3.4 13.9 - - + +
11I THR* 1.3 76.9 - - - +
13I ARG* 1.3 50.7 - - - +
15I GLN* 3.3 5.6 - - - +
16I HIS* 2.2 46.0 + - + +
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Residues in contact with ARG 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLU* 4.2 10.2 + - - +
127C HIS* 2.5 30.1 + - - +
128C VAL* 3.6 3.8 - - - +
132C ASP* 2.6 50.7 + - - +
9I ALA 3.0 16.3 + - - +
10I ALA* 3.8 7.6 - - - +
12I ALA* 1.3 73.6 - - - +
14I ARG* 1.3 52.8 + - - +
15I GLN 2.4 10.7 + - - -
16I HIS* 2.4 19.2 + - + -
17I LEU* 2.1 60.4 + - + +
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Residues in contact with ARG 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ASP* 3.2 39.9 + - - +
136C LEU* 3.7 31.4 - - + +
139C ASP* 4.5 23.6 + - - +
7I ARG* 5.6 6.7 - - - +
10I ALA* 3.2 34.0 + - - +
11I THR* 2.8 41.8 + - + +
13I ARG* 1.3 75.7 - - - +
15I GLN* 1.3 50.2 + - - +
17I LEU* 3.3 16.4 - - + +
18I LYS* 2.7 47.7 + - - +
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Residues in contact with GLN 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C MET 4.5 0.5 - - - +
158C GLU 4.4 14.7 + - - -
159C GLY* 5.7 2.0 - - - -
160C VAL* 4.3 11.8 - - + +
11I THR* 2.4 48.9 + - + +
12I ALA* 3.5 5.4 - - - +
13I ARG 2.4 9.1 + - - -
14I ARG* 1.3 64.8 - - - +
16I HIS* 1.3 62.0 + - - +
17I LEU 2.7 5.5 + - - -
18I LYS* 3.1 36.8 + - - +
19I SER* 2.9 23.4 + - - -
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Residues in contact with HIS 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLU* 3.6 33.6 + - + +
12I ALA* 2.2 40.0 + - + +
13I ARG* 2.4 17.1 + - + +
15I GLN* 1.3 67.2 - - - +
17I LEU* 1.3 54.7 + - + +
19I SER* 3.2 20.5 + - - -
20I ALA* 4.0 4.0 + - - +
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 4.2 16.1 - - + +
124C THR* 6.3 0.2 - - + -
126C GLU* 4.2 15.7 - - + -
128C VAL* 3.7 28.5 - - + -
132C ASP* 5.0 8.5 - - + +
136C LEU* 4.9 7.2 - - + -
13I ARG* 2.1 67.1 + - + +
14I ARG* 3.3 30.1 - - + +
16I HIS* 1.3 65.3 - - - +
18I LYS* 1.3 54.7 + - - +
19I SER 2.6 4.6 + - - -
20I ALA* 2.3 39.7 + - + +
21I MET* 3.3 4.6 + - - +
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Residues in contact with LYS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU* 3.8 19.5 - - + +
139C ASP* 3.9 15.7 + - - -
156C MET* 3.1 63.4 + - + +
157C MET* 3.6 18.6 - - + -
160C VAL* 3.9 14.1 - - + -
14I ARG* 2.7 32.4 + - - +
15I GLN* 3.1 27.2 + - - +
17I LEU* 1.3 72.3 - - - +
19I SER* 1.3 61.2 + - - +
20I ALA 3.0 0.2 - - - -
21I MET* 3.1 23.5 + - - +
22I LEU* 3.3 18.9 + - - +
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Residues in contact with SER 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 3.5 17.5 - - - +
161C GLN* 3.7 13.3 + - - +
15I GLN 2.9 12.7 + - - -
16I HIS* 3.2 23.6 + - - -
17I LEU 2.6 0.4 + - - -
18I LYS* 1.3 78.9 - - - +
20I ALA* 1.3 55.6 + - - -
22I LEU* 4.5 1.4 - - - +
23I GLN* 3.0 35.8 + - - +
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 5.7 2.2 - - + -
124C THR* 3.5 34.6 + - + +
126C GLU* 4.6 14.4 - - + -
16I HIS 4.0 2.4 + - - +
17I LEU* 2.3 34.3 + - + +
19I SER* 1.3 68.6 - - - +
21I MET* 1.3 67.0 + - + +
23I GLN* 3.2 12.2 + - - +
24I LEU* 3.2 19.4 + - - +
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Residues in contact with MET 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 2.8 46.0 - - + -
112C ILE* 6.1 4.3 - - + -
117C LEU* 3.7 33.2 - - + -
120C ILE* 4.0 21.3 - - + -
121C LEU* 4.6 13.0 - - + -
124C THR* 5.7 0.2 - - - -
136C LEU* 4.7 5.8 - - + -
153C PHE* 5.9 1.8 - - + -
156C MET* 4.6 8.5 - - + -
157C MET* 3.6 28.5 - - + -
17I LEU 3.3 1.7 + - - +
18I LYS* 3.1 17.5 + - - +
20I ALA* 1.3 80.5 - - - +
22I LEU* 1.3 62.0 + - - +
24I LEU* 3.0 16.2 + - - +
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Residues in contact with LEU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU* 5.3 6.5 - - + -
100C CYS* 4.1 19.6 - - + -
104C PHE* 3.5 18.8 - - + -
153C PHE* 5.1 0.4 - - + -
157C MET* 3.2 38.8 - - + +
160C VAL* 3.7 44.9 - - + +
161C GLN* 4.5 7.4 - - + +
18I LYS 3.3 9.9 + - - +
19I SER 4.5 1.8 - - - +
21I MET* 1.3 75.2 - - - +
23I GLN* 1.3 53.9 + - - +
24I LEU 2.4 18.7 + - - -
25I ALA* 2.8 13.4 + - - -
26I VAL* 2.9 14.4 + - - +
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Residues in contact with GLN 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C THR* 5.8 1.5 + - - +
19I SER* 3.0 30.1 + - - +
20I ALA* 3.2 11.4 + - - +
22I LEU* 1.3 76.5 - - - +
24I LEU* 1.3 55.6 + - - +
26I VAL* 2.7 26.2 - - + +
27I THR* 3.9 5.7 - - - +
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Residues in contact with LEU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE* 6.2 0.7 - - + -
120C ILE* 3.2 34.3 - - + +
123C ALA* 2.9 42.8 - - + +
124C THR* 3.5 16.2 - - - +
20I ALA 3.2 4.4 + - - +
21I MET 3.0 10.9 + - - +
22I LEU 2.4 11.3 + - - -
23I GLN* 1.3 71.1 - - - +
25I ALA* 1.3 64.7 + - - +
26I VAL 3.0 1.3 - - - -
27I THR* 2.8 32.6 - - + +
28I GLU* 2.9 16.1 + - + +
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Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C CYS* 4.1 13.5 - - - -
103C ILE* 2.8 43.8 - - + +
104C PHE* 3.4 31.7 - - + -
21I MET 3.4 1.0 + - - -
22I LEU 2.8 6.2 + - - +
24I LEU* 1.3 75.2 - - - +
26I VAL* 1.3 52.7 + - - +
28I GLU 2.9 0.3 + - - -
29I ILE* 2.7 33.7 + - - +
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Residues in contact with VAL 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C CYS* 5.1 4.4 - - - -
22I LEU 2.9 8.0 + - - +
23I GLN* 2.7 40.4 - - + +
25I ALA* 1.3 76.5 - - - +
27I THR* 1.3 71.3 + - + +
29I ILE* 2.8 33.5 + - - +
30I GLU* 3.7 4.2 + - - +
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Residues in contact with THR 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLN 3.9 9.0 - - - +
24I LEU* 2.8 33.2 - - + +
26I VAL* 1.3 87.6 - - - +
28I GLU* 1.3 63.9 + - + +
29I ILE 3.1 1.0 + - - -
30I GLU* 3.4 21.7 + - - +
31I LYS* 3.6 24.0 - - - +
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE* 3.1 39.6 - - + +
106C LYS* 4.9 12.2 + - - +
24I LEU* 2.9 21.3 + - + +
25I ALA* 2.9 4.1 + - - +
27I THR* 1.3 78.0 - - + +
29I ILE* 1.3 62.1 + - - +
31I LYS* 3.0 40.8 + - - +
32I GLU* 3.8 16.8 + - + +
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Residues in contact with ILE 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLU* 5.2 5.4 - - + +
99C ASN* 3.2 42.2 - - + +
100C CYS* 4.8 4.9 - - - +
102C ARG* 4.5 11.2 + - - +
103C ILE* 3.1 25.4 - - + -
25I ALA 2.7 10.1 + - - +
26I VAL* 2.8 17.3 + - - +
28I GLU* 1.3 81.1 - - - +
30I GLU* 1.3 62.8 + - + +
31I LYS 3.0 5.8 + - - -
32I GLU* 3.7 9.4 + - - +
33I ALA* 3.7 13.7 + - + +
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Residues in contact with GLU 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I VAL 3.7 2.0 + - - +
27I THR* 3.4 18.8 + - - +
29I ILE* 1.3 81.2 - - + +
31I LYS* 1.3 58.4 + - + +
33I ALA* 4.1 9.9 - - - -
34I ALA* 3.6 20.6 + - - +
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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
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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