Contacts of the helix formed by residues 0 - 21 (chain A) in PDB entry 2P1A
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 GLY 0 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 1.3 60.7 - - - +
2A PHE* 4.0 6.9 - - - +
3A VAL* 3.9 27.4 - - - +
4A GLN* 3.1 39.5 + - - +
97A LEU* 5.8 0.6 - - - +
101A ASN* 5.1 4.9 + - - -
104A LEU* 4.9 5.9 - - - +
2B PHE* 5.5 2.2 - - - -
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Residues in contact with MSE 1 (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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0A GLY* 1.3 71.9 - - - +
2A PHE* 1.3 91.0 + - + +
4A GLN* 3.9 6.6 - - - +
5A SER* 2.7 41.2 + - - +
101B ASN* 4.3 17.5 - - + +
104B LEU 4.9 2.0 - - - +
105B ALA* 4.1 35.4 - - + -
117B SER* 5.9 1.1 - - - -
119B PHE* 5.4 3.4 - - + -
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Residues in contact with PHE 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY 3.3 3.7 - - - +
1A MSE 1.3 104.4 - - + +
3A VAL* 1.3 62.3 + - - +
5A SER* 3.4 3.9 + - - -
6A ALA* 3.1 23.6 + - - +
119A PHE* 3.9 4.1 - - + -
0B GLY 5.5 1.6 - - - -
2B PHE* 3.6 54.1 - + + -
3B VAL* 5.2 0.2 - - + -
101B ASN* 3.9 26.9 - - - -
104B LEU* 4.0 22.0 - - + -
119B PHE* 3.5 55.2 - + + -
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY* 3.8 15.3 + - - +
1A MSE 3.5 0.2 - - - -
2A PHE* 1.3 74.5 - - - +
4A GLN* 1.3 58.8 + - - +
6A ALA* 3.2 2.6 + - - +
7A LEU* 2.9 47.6 + - + +
96A PHE* 3.8 28.3 - - + +
97A LEU* 4.5 6.5 - - + -
104A LEU* 3.5 41.3 - - + -
119A PHE* 4.0 16.6 - - + -
122A LEU* 4.0 7.0 - - + -
2B PHE* 4.8 1.6 - - + -
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Residues in contact with GLN 4 (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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0A GLY* 3.1 23.9 + - - +
1A MSE 3.9 5.3 - - - +
3A VAL* 1.3 75.6 - - - +
5A SER* 1.3 57.3 + - - +
7A LEU* 3.9 6.6 - - + +
8A HIS* 3.0 29.8 + - - +
97A LEU* 4.3 24.2 - - + +
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Residues in contact with SER 5 (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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1A MSE 2.7 28.1 + - - +
2A PHE 3.5 5.8 - - - -
3A VAL 3.3 0.2 - - - -
4A GLN* 1.3 75.1 - - - +
6A ALA* 1.3 62.3 + - - +
8A HIS* 3.2 7.7 + - - +
9A GLN* 3.1 22.9 + - - +
117B SER* 4.7 1.4 + - - -
119B PHE* 3.9 11.1 - - - +
120B GLU* 3.6 35.1 + - - +
123B LEU* 3.7 14.2 - - - +
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Residues in contact with ALA 6 (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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2A PHE 3.1 16.9 + - - +
3A VAL 3.7 0.2 - - - +
5A SER* 1.3 76.6 - - - +
7A LEU* 1.3 59.6 + - - +
9A GLN* 3.5 5.6 - - - +
10A LEU* 3.2 18.2 + - - +
119A PHE* 4.5 2.2 - - + -
122A LEU* 3.7 27.1 - - + +
123A LEU* 3.7 27.8 - - + -
126A VAL* 3.7 11.0 - - + +
123B LEU* 3.5 11.4 - - + +
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Residues in contact with LEU 7 (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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3A VAL* 2.9 36.8 + - + +
4A GLN* 4.0 5.8 - - + +
6A ALA* 1.3 73.2 - - - +
8A HIS* 1.3 60.8 + - - +
10A LEU* 3.5 7.5 + - + -
11A LYS 2.9 22.7 + - - -
89A TYR* 3.3 27.4 + - + +
92A LEU 4.5 4.3 - - - +
93A SER* 3.9 33.0 - - - +
96A PHE* 4.4 2.2 - - + -
97A LEU* 3.9 28.9 - - + -
122A LEU* 3.8 29.4 - - + -
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Residues in contact with HIS 8 (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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4A GLN 3.0 18.2 + - - +
5A SER* 3.2 6.7 + - - +
7A LEU* 1.3 72.8 - - - +
9A GLN* 1.3 68.0 + - - +
11A LYS* 3.7 11.5 - - + +
12A VAL* 3.0 49.8 + - + +
89A TYR* 5.0 0.7 - - - -
120B GLU* 6.0 3.8 - - - +
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Residues in contact with GLN 9 (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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5A SER 3.1 13.2 + - - +
6A ALA* 3.5 13.7 - - - +
8A HIS* 1.3 80.3 + - - +
10A LEU* 1.3 60.5 + - - +
12A VAL* 3.7 4.0 + - - +
13A ALA* 3.3 17.2 + - - +
126A VAL* 3.7 24.5 - - + -
130A TYR* 3.3 35.4 + - + -
120B GLU* 4.0 2.4 - - - +
123B LEU* 3.7 22.9 - - + +
124B GLU* 2.9 45.2 + - - +
127B ALA* 3.5 18.0 - - - +
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Residues in contact with LEU 10 (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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6A ALA 3.2 11.1 + - - +
7A LEU* 3.7 10.3 - - + +
8A HIS 3.2 0.2 - - - -
9A GLN* 1.3 78.8 - - - +
11A LYS* 1.3 59.4 + - - +
13A ALA* 3.2 6.8 + - + +
14A VAL* 2.9 29.3 + - + +
51A CYS* 4.0 14.8 - - - -
89A TYR* 4.0 19.1 - - + -
92A LEU* 3.3 35.4 - - + -
122A LEU* 4.7 9.0 - - + -
125A ILE* 4.6 6.3 - - + -
126A VAL* 4.2 19.9 - - + +
129A PHE* 4.1 33.0 - - + -
130A TYR* 5.3 1.1 - - + -
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Residues in contact with LYS 11 (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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7A LEU 2.9 18.7 + - - +
8A HIS* 3.2 14.1 + - + +
10A LEU* 1.3 74.8 - - - +
12A VAL* 1.3 53.9 + - + +
14A VAL* 3.4 3.2 + - + +
15A ASP* 2.7 62.7 + - - +
86A ILE* 6.4 1.1 - - - -
89A TYR* 3.5 41.5 - - + +
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Residues in contact with VAL 12 (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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8A HIS* 3.0 48.9 + - + +
9A GLN* 3.9 6.1 - - - +
11A LYS* 1.3 74.7 - - + +
13A ALA* 1.3 53.9 + - - +
15A ASP* 3.8 5.3 - - - +
16A THR* 2.7 49.4 + - + +
130A TYR* 4.5 7.2 - - - +
124B GLU* 6.1 0.9 - - - +
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Residues in contact with ALA 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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9A GLN 3.3 6.4 + - - +
10A LEU* 3.2 11.8 + - + +
12A VAL* 1.3 78.8 - - - +
14A VAL* 1.3 55.2 + - - +
16A THR* 2.8 18.5 + - - -
17A SER* 2.9 21.7 + - - -
129A PHE* 3.6 26.2 - - + -
130A TYR* 3.5 34.0 + - + +
133A ARG* 3.8 4.7 + - - +
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Residues in contact with VAL 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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10A LEU* 2.9 33.3 + - + +
11A LYS* 3.7 5.6 - - + +
13A ALA* 1.3 75.5 - - - +
15A ASP* 1.3 61.8 + - - +
17A SER* 3.1 4.2 + - - -
18A ILE* 2.9 48.6 + - + +
51A CYS* 4.6 6.5 - - - -
85A MSE 3.8 25.6 - - + +
86A ILE* 4.6 4.5 - - + -
89A TYR* 4.5 17.0 - - + -
129A PHE* 3.9 27.1 - - + -
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Residues in contact with ASP 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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11A LYS* 2.7 52.4 + - - +
12A VAL* 4.0 5.7 - - - +
14A VAL* 1.3 74.4 - - - +
16A THR* 1.3 61.1 + - + +
18A ILE* 3.6 8.5 + - - +
19A GLN* 3.3 26.0 + - - +
86A ILE* 4.2 19.2 - - - +
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 2.7 36.6 + - + +
13A ALA* 2.8 14.2 + - - -
15A ASP* 1.3 72.5 - - + +
17A SER* 1.3 58.9 + - - +
19A GLN* 3.3 22.1 - - - +
20A MSE 2.9 38.6 + - - +
133A ARG* 3.0 27.9 + - - +
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Residues in contact with SER 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 ALA 2.9 18.7 + - - -
14A VAL 3.5 7.9 - - - -
16A THR* 1.3 76.6 + - - +
18A ILE* 1.3 60.0 + - - +
20A MSE 3.5 11.1 + - - +
21A LEU* 3.2 28.8 + - - +
44A TYR* 4.2 4.8 - - - -
47A LEU* 3.7 11.6 - - - +
85A MSE 3.7 22.9 - - - -
129A PHE* 3.4 8.3 - - - -
133A ARG* 3.3 20.5 - - - +
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Residues in contact with ILE 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 VAL* 2.9 30.5 + - + +
15A ASP* 3.8 10.3 - - - +
17A SER* 1.3 76.1 - - - +
19A GLN* 1.3 61.0 + - - +
21A LEU* 3.3 6.2 + - - +
22A ASP* 3.6 4.0 + - - +
82A GLN* 2.8 53.6 + - + +
85A MSE 3.4 22.0 - - + -
86A ILE* 3.4 40.4 - - + -
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Residues in contact with GLN 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 ASP 3.3 14.5 + - - +
16A THR* 3.3 31.8 - - - +
18A ILE* 1.3 77.1 - - - +
20A MSE 1.3 65.8 - - + +
22A ASP* 3.2 20.2 + - - +
23A GLN* 3.0 27.8 + - - +
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Residues in contact with MSE 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 THR* 2.9 25.6 + - - +
17A SER* 3.7 7.6 - - - +
19A GLN* 1.3 78.7 - - + +
21A LEU* 1.3 58.6 + - - +
23A GLN* 3.2 15.7 + - + +
24A TYR* 3.1 28.7 - - + -
44A TYR* 3.2 37.9 - - + +
133A ARG* 4.2 33.9 - - + +
136A ILE* 4.7 5.2 - - + -
137A HIS* 5.1 13.0 - - + -
140A LEU* 3.3 25.8 - - + -
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Residues in contact with LEU 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 SER 3.2 12.1 + - - +
18A ILE 3.5 8.1 - - - +
19A GLN 3.2 0.6 - - - -
20A MSE 1.3 74.3 - - - +
22A ASP* 1.3 60.8 + - - +
23A GLN 3.3 0.2 - - - -
24A TYR* 3.3 20.7 + - - +
29A LEU* 4.0 17.0 - - + -
44A TYR* 3.5 47.8 - - + +
78A ILE* 3.7 21.3 - - + +
81A MSE 4.0 22.7 - - + -
82A GLN* 3.7 21.8 - - + +
85A MSE 3.7 29.2 - - + -
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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