Contacts of the helix formed by residues 12 - 26 (chain A) in PDB entry 4P7A
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 ASP 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG 3.6 1.6 + - - -
11A LEU* 1.3 69.6 - - - +
13A GLU* 1.3 58.4 + - - +
14A THR* 2.4 53.6 + - - +
15A VAL* 3.3 19.1 + - + +
16A VAL* 3.2 21.5 + - - +
408A UNX 3.3 15.1 - - - -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 6.1 1.6 - - - +
11A LEU* 3.3 10.9 + - + +
12A ASP* 1.3 71.6 + - - +
14A THR* 1.3 61.7 + - + +
15A VAL 3.3 0.2 - - - -
16A VAL* 3.7 19.3 - - + -
17A ASN* 2.8 49.0 + - - +
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 2.4 42.4 + - - +
13A GLU* 1.3 72.0 - - - +
15A VAL* 1.3 61.8 + - - +
17A ASN* 4.3 3.7 - - - +
18A ARG* 3.4 33.5 + - - +
109A HIS* 5.3 3.4 - - - -
132A ASP* 5.9 4.7 - - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 3.3 24.7 + - + +
14A THR* 1.3 76.9 + - - +
16A VAL* 1.3 67.1 + - + +
18A ARG* 3.2 30.5 + - - +
19A ILE* 3.0 43.1 + - + +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 32.5 - - + -
12A ASP 3.2 13.2 + - - +
13A GLU* 3.7 15.2 - - + -
14A THR 3.5 0.4 - - - -
15A VAL* 1.3 78.9 - - + +
17A ASN* 1.3 65.8 + - - +
19A ILE* 3.2 5.1 + - - +
20A ALA* 3.0 32.9 + - + +
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 2.8 43.4 + - - +
14A THR* 4.3 3.4 - - - +
16A VAL* 1.3 81.3 - - - +
18A ARG* 1.3 61.0 + - - +
20A ALA* 4.2 3.8 - - - +
21A ALA* 3.1 29.6 + - - +
79A ARG* 5.5 9.4 + - - -
109A HIS* 3.7 30.7 + - + +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.4 31.6 + - - +
15A VAL* 3.2 35.3 + - - +
17A ASN* 1.3 78.3 - - - +
19A ILE* 1.3 67.5 + - - +
21A ALA* 3.4 3.6 + - - +
22A GLY 3.1 17.8 + - - -
109A HIS* 4.0 16.3 - - + +
110A VAL* 3.7 0.2 - - - +
132A ASP* 5.9 1.3 + - - +
158A ASN* 3.1 52.1 + - - +
159A ILE* 3.5 23.1 - - + +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.0 37.0 + - + +
16A VAL* 3.9 4.5 - - - +
18A ARG* 1.3 84.5 - - + +
20A ALA* 1.3 63.5 + - - +
22A GLY* 3.3 3.6 + - - -
23A GLU* 3.2 21.6 + - + +
159A ILE* 4.9 13.5 - - + -
162A ARG* 5.0 4.0 + - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.0 21.7 + - + +
17A ASN* 4.2 5.6 - - - +
19A ILE* 1.3 74.7 - - - +
21A ALA* 1.3 66.3 + - - +
23A GLU* 3.0 19.1 + - - +
24A VAL* 3.1 18.9 + - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN 3.1 21.4 + - - +
18A ARG 3.6 4.3 - - - +
20A ALA* 1.3 76.3 - - - +
22A GLY* 1.3 62.3 + - - +
24A VAL* 3.2 3.0 + - - +
25A ILE* 3.0 28.9 + - - +
106A SER* 3.3 44.2 - - - +
109A HIS* 3.8 9.6 - - + -
110A VAL* 4.0 5.4 - - + -
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG 3.1 13.5 + - - -
19A ILE 3.3 5.3 + - - -
21A ALA* 1.3 75.5 - - - +
23A GLU* 1.3 56.5 + - - +
26A GLN* 2.9 31.2 + - - -
110A VAL* 3.9 1.6 - - - +
156A PHE* 4.1 14.8 - - - -
159A ILE* 4.2 4.5 - - - -
162A ARG* 3.5 28.3 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.2 13.2 + - + +
20A ALA* 3.0 15.1 + - - +
22A GLY* 1.3 76.7 - - - +
24A VAL* 1.3 62.3 + - + +
26A GLN* 4.7 5.9 - - - +
162A ARG* 3.0 30.0 + - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.1 16.4 + - + +
21A ALA 3.2 5.8 + - - +
23A GLU* 1.3 79.0 - - + +
25A ILE* 1.3 73.0 - - + +
26A GLN* 4.4 1.6 - - - +
30A ASN* 2.9 20.4 + - - +
34A GLU* 5.6 7.4 - - + +
102A GLU* 5.7 6.3 - - + +
103A ALA* 5.9 3.4 - - - -
106A SER* 4.2 19.1 - - - +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.0 17.1 + - - +
24A VAL* 1.3 80.5 - - + +
26A GLN* 1.3 66.0 + - - +
27A ARG 2.9 22.2 + - - +
30A ASN* 2.8 28.8 + - - +
31A ALA* 4.0 22.2 - - + +
34A GLU* 5.2 8.7 - - + -
103A ALA* 4.5 2.9 - - - +
106A SER* 4.1 20.0 - - - -
107A ILE* 3.4 33.7 - - + +
110A VAL* 4.6 2.9 - - + -
155A LEU* 4.5 11.4 - - + -
156A PHE* 4.3 14.4 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 2.9 19.8 + - - +
23A GLU 4.7 4.9 - - - +
24A VAL 4.4 4.3 - - - +
25A ILE* 1.3 79.3 - - - +
27A ARG* 1.3 67.0 + - + +
30A ASN* 4.8 2.2 - - + +
156A PHE* 3.4 15.7 - - - -
162A ARG* 4.5 18.0 + - - +
166A LEU* 3.3 14.4 - - - +
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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
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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