Contacts of the helix formed by residues 10 - 25 (chain X) in PDB entry 1V7M
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 10 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8X ASP* 3.2 36.3 + - + -
9X LEU* 1.3 78.5 - - - +
11X VAL* 1.3 59.4 + - - +
12X LEU 3.1 0.7 - - - -
13X SER* 3.4 20.0 - - - +
14X LYS* 2.7 58.1 + - - +
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Residues in contact with VAL 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ASP* 3.3 31.3 + - - +
9X LEU 3.4 0.6 - - - -
10X ARG* 1.3 79.5 - - - +
12X LEU* 1.3 54.5 + - - +
14X LYS* 4.8 3.1 - - - -
15X LEU* 2.7 60.8 + - + +
99X LEU 6.0 0.9 - - - +
100X LEU* 5.4 2.7 - - + -
103X ALA* 5.1 10.5 - - + -
143X MET* 4.2 19.3 - - + -
150X LEU* 4.3 6.5 - - + -
151X CYS* 3.7 28.0 - - + +
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Residues in contact with LEU 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 4.1 9.0 + - + +
10X ARG* 4.0 0.2 - - - +
11X VAL* 1.3 84.1 - - - +
13X SER* 1.3 57.9 + - - +
15X LEU* 3.3 7.1 + - - +
16X LEU* 2.7 52.3 + - + +
135X LEU* 3.3 33.2 - - + +
139X VAL* 3.8 22.0 - - + -
140X ARG* 4.5 22.4 - - + +
143X MET* 3.5 24.7 - - + -
144X LEU* 5.8 5.8 - - + -
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Residues in contact with SER 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU 3.9 4.7 + - - -
10X ARG* 3.1 26.5 + - - +
12X LEU* 1.3 80.9 - - - +
14X LYS* 1.3 66.0 + - - +
16X LEU* 3.4 5.4 + - - +
17X ARG* 3.2 23.9 + - - +
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Residues in contact with LYS 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ARG* 2.7 44.1 + - - +
11X VAL* 4.3 2.0 - - - +
13X SER* 1.3 71.0 - - - +
15X LEU* 1.3 73.5 + - + +
17X ARG* 3.1 13.8 - - + +
18X ASP* 2.7 56.1 + - - +
96X GLN* 6.3 1.6 - - - -
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Residues in contact with LEU 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X VAL* 2.7 43.7 + - + +
12X LEU* 3.4 5.8 - - - +
13X SER 3.3 0.2 - - - -
14X LYS* 1.3 89.3 - - + +
16X LEU* 1.3 60.7 + - - +
18X ASP* 4.9 1.1 - - - -
19X SER* 3.3 23.2 + - - -
96X GLN* 3.8 23.8 - - + +
99X LEU* 4.5 21.8 - - + -
100X LEU* 4.3 25.8 - - + +
131X PHE* 5.0 3.8 - - + -
135X LEU* 4.0 33.7 - - + +
143X MET* 5.9 0.2 - - + -
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Residues in contact with LEU 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X LEU* 2.7 49.6 + - + +
13X SER* 4.0 5.2 - - - +
14X LYS 3.3 0.4 - - - -
15X LEU* 1.3 69.6 - - - +
17X ARG* 1.3 69.1 - - - +
19X SER* 3.5 18.5 + - - -
20X HIS* 3.6 6.1 + - - +
132X GLN* 4.8 11.0 - - + +
135X LEU* 4.1 28.5 - - + +
136X ARG* 5.0 9.0 - - - +
140X ARG* 4.1 20.9 - - - +
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Residues in contact with ARG 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X SER 3.2 12.5 + - - +
14X LYS* 3.1 16.2 - - - +
16X LEU* 1.3 77.1 - - - +
18X ASP* 1.3 68.6 + - - +
20X HIS* 3.3 4.2 + - - +
21X VAL* 3.2 33.6 + - - +
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Residues in contact with ASP 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X LYS* 2.7 58.7 + - - +
15X LEU* 4.4 0.9 - - - +
17X ARG* 1.3 84.5 - - - +
19X SER* 1.3 67.9 + - - +
21X VAL* 3.0 12.7 + - + -
22X LEU* 2.7 27.6 + - + +
96X GLN* 3.1 32.1 + - - +
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Residues in contact with SER 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X LEU 3.3 17.0 + - - -
16X LEU* 3.5 12.8 - - - -
17X ARG 3.3 0.4 - - - -
18X ASP* 1.3 74.2 - - - +
20X HIS* 1.3 58.1 + - - +
22X LEU* 3.5 4.6 + - - +
23X HIS* 2.9 27.6 + - - +
93X LEU* 5.5 3.9 - - - +
96X GLN* 3.1 14.3 + - - -
128X PHE* 4.6 5.4 + - - -
131X PHE* 4.1 15.8 - - - -
132X GLN* 3.3 28.2 - - - +
135X LEU* 4.5 8.1 - - - -
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Residues in contact with HIS 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LEU 3.6 4.1 + - - +
17X ARG* 3.3 7.4 + - - +
18X ASP 3.2 0.4 - - - -
19X SER* 1.3 75.5 - - - +
21X VAL* 1.3 71.6 + - - +
23X HIS* 3.9 21.3 - + - +
24X SER* 2.9 36.6 + - - -
129X LEU* 6.3 0.4 - - + -
132X GLN* 2.7 30.8 + - - +
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Residues in contact with VAL 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ARG* 3.2 36.3 + - - +
18X ASP* 3.0 11.8 + - + +
20X HIS* 1.3 76.8 - - - +
22X LEU* 1.3 61.5 + - + +
24X SER* 3.4 1.7 + - - -
25X ARG* 2.6 57.7 + - - +
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Residues in contact with LEU 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ASP* 2.7 16.7 + - + +
19X SER* 3.7 4.0 - - - +
21X VAL* 1.3 73.0 - - + +
23X HIS* 1.3 67.6 + - - +
25X ARG* 3.1 27.7 + - - +
89X LEU* 3.4 37.9 - - + +
92X GLN* 3.6 47.3 - - + +
93X LEU* 3.9 10.1 - - + +
96X GLN* 3.4 30.7 - - - +
128X PHE* 4.0 8.0 - - + -
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Residues in contact with HIS 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X SER 2.9 19.1 + - - +
20X HIS* 3.1 25.7 + + - +
22X LEU* 1.3 71.9 - - - +
24X SER* 1.3 64.6 - - - +
26X LEU* 3.0 32.7 + - + +
125X ASN* 2.5 35.4 + - - -
128X PHE* 3.5 34.5 - - + +
129X LEU* 4.6 11.1 - - + +
132X GLN* 3.6 24.7 + - - +
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Residues in contact with SER 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X HIS* 2.9 29.4 + - - -
21X VAL* 3.6 5.8 - - - -
23X HIS* 1.3 76.8 - - - +
25X ARG* 1.3 61.2 + - - +
26X LEU* 2.8 12.1 + - - +
27X SER* 3.2 19.9 + - - -
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Residues in contact with ARG 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X VAL* 2.6 54.5 + - - +
22X LEU* 3.1 23.7 + - - +
24X SER* 1.3 80.9 - - - +
26X LEU* 1.3 57.7 + - - +
27X SER* 3.1 3.3 + - - -
28X GLN* 3.5 45.3 - - - +
29X CYS* 5.5 0.3 - - - -
85X CYS* 5.5 0.5 - - - -
89X LEU* 3.6 21.1 - - + +
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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
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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