Contacts of the helix formed by residues 3 - 24 (chain A) in PDB entry 2FD5
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 84.1 + - - +
4A LYS* 1.3 61.1 + - - +
5A LYS* 2.9 14.0 + - - +
6A THR* 2.5 45.0 + - - -
7A GLN* 3.0 30.3 + - - +
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Residues in contact with LYS 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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3A ASP* 1.3 76.9 - - - +
5A LYS* 1.3 58.7 + - - +
7A GLN* 3.9 19.1 + - - +
8A THR* 2.8 39.4 + - - +
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Residues in contact with LYS 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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3A ASP* 2.9 9.0 + - - +
4A LYS* 1.3 76.7 - - - +
6A THR* 1.3 66.9 + - - +
8A THR* 3.3 1.3 + - - -
9A ARG* 3.0 24.5 + - + +
46A ALA 5.5 5.8 - - - -
47A HIS* 3.7 24.9 - - + +
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Residues in contact with THR 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 SER* 3.6 15.5 - - - +
3A ASP* 2.5 34.0 + - - -
5A LYS* 1.3 72.7 - - - +
7A GLN* 1.3 62.2 + - - +
9A ARG* 3.5 5.8 + - - +
10A ALA* 3.0 25.8 + - + +
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Residues in contact with GLN 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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2A SER* 4.3 14.4 + - - +
3A ASP 3.0 18.2 + - - +
4A LYS* 3.9 21.1 + - - +
6A THR* 1.3 77.0 - - - +
8A THR* 1.3 57.4 + - - +
10A ALA* 3.3 7.6 + - + +
11A ARG* 2.9 46.2 + - + +
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Residues in contact with THR 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 LYS* 2.8 26.8 + - - +
5A LYS* 3.8 3.6 - - - -
7A GLN* 1.3 73.9 - - - +
9A ARG* 1.3 64.9 + - - +
11A ARG* 3.2 18.3 + - - +
12A ILE* 3.0 22.6 + - + +
34A MET* 6.0 0.2 - - + -
39A LEU* 3.8 26.8 - - + +
47A HIS* 3.4 27.6 - - + +
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Residues in contact with ARG 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 LYS* 3.0 17.4 + - + +
6A THR* 3.8 5.8 - - - +
8A THR* 1.3 75.3 - - - +
10A ALA* 1.3 58.8 + - - +
12A ILE* 3.1 6.2 + - - +
13A LEU* 2.9 37.0 + - - +
47A HIS* 3.8 30.8 + - + +
48A PHE* 3.5 31.7 - - + -
57A GLU* 2.8 43.2 + - - -
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Residues in contact with ALA 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 THR* 3.0 19.1 + - + +
7A GLN* 3.3 8.3 + - + +
9A ARG* 1.3 78.4 - - - +
11A ARG* 1.3 56.9 + - - +
13A LEU* 3.8 7.0 - - - +
14A GLY* 2.8 26.9 + - - -
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Residues in contact with ARG 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 GLN* 2.9 34.0 + - + +
8A THR* 3.2 14.8 + - - +
10A ALA* 1.3 72.3 - - + +
12A ILE* 1.3 65.3 + - - +
14A GLY* 3.8 1.6 - - - -
15A ALA* 3.1 24.1 + - - +
37A ALA* 2.7 36.3 + - + +
38A GLY* 3.4 16.6 + - - -
39A LEU* 3.6 24.8 - - + +
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Residues in contact with ILE 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 THR* 3.0 15.1 + - + +
9A ARG 3.1 6.0 + - - +
11A ARG* 1.3 74.1 - - - +
13A LEU* 1.3 57.5 + - - +
15A ALA* 3.3 2.4 + - - -
16A ALA* 2.9 25.8 + - - +
33A VAL* 3.6 11.8 - - + +
34A MET* 3.6 31.2 - - + -
37A ALA* 4.5 5.8 - - - -
39A LEU* 3.4 24.7 - - + -
44A PHE* 4.3 8.7 - - + -
47A HIS* 3.7 38.8 - - + -
48A PHE* 3.5 22.9 - - + -
54A LEU* 3.9 9.6 - - + -
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Residues in contact with LEU 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 ARG* 2.9 23.4 + - - +
10A ALA* 3.9 7.4 - - - +
12A ILE* 1.3 76.8 - - - +
14A GLY* 1.3 56.2 + - - +
16A ALA* 3.5 3.8 - - - +
17A THR* 2.8 36.9 + - + +
48A PHE* 4.4 5.4 - - + -
54A LEU* 4.0 19.7 - - + +
57A GLU* 3.6 28.3 - - + +
58A ALA* 3.8 31.2 - - + +
61A GLN* 3.4 36.3 - - - +
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Residues in contact with GLY 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 ALA 2.8 17.4 + - - -
11A ARG* 3.8 2.5 - - - -
13A LEU* 1.3 76.5 - - - +
15A ALA* 1.3 59.7 + - - +
17A THR* 2.8 22.0 + - - -
18A GLN* 3.2 16.9 + - - +
61A GLN* 6.0 0.2 - - - -
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Residues in contact with ALA 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 ARG 3.1 16.9 + - - +
12A ILE 3.6 4.3 - - - +
14A GLY* 1.3 75.3 - - - +
16A ALA* 1.3 62.8 + - - +
18A GLN* 3.5 7.2 + - - +
19A ALA* 3.1 24.1 + - - +
33A VAL* 3.5 32.0 - - + +
36A ALA* 4.2 13.7 - - + +
37A ALA* 4.0 12.8 - - + +
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Residues in contact with ALA 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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12A ILE 2.9 15.1 + - - +
13A LEU* 3.2 8.3 + - - +
15A ALA* 1.3 73.9 - - - +
17A THR* 1.3 60.7 + - - +
19A ALA* 3.3 2.8 + - - +
20A LEU* 2.9 30.1 + - - +
33A VAL* 3.8 11.4 - - + +
54A LEU* 3.7 37.5 - - + -
55A MET* 3.9 11.3 - - - +
58A ALA* 4.4 7.2 - - + -
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Residues in contact with THR 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 LEU* 2.8 23.9 + - + +
14A GLY* 2.8 24.0 + - - -
16A ALA* 1.3 71.4 - - - +
18A GLN* 1.3 59.9 + - - +
20A LEU* 3.3 2.2 + - - +
21A LEU* 2.9 36.6 + - - +
58A ALA* 3.6 33.4 - - + +
61A GLN* 3.6 23.3 - - - +
62A LEU* 3.8 21.6 - - + +
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Residues in contact with GLN 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 GLY 3.2 16.0 + - - +
15A ALA* 3.7 7.2 - - - +
16A ALA 3.2 0.2 - - - -
17A THR* 1.3 85.0 + - - +
19A ALA* 1.3 61.6 + - - +
21A LEU* 3.4 23.3 + - - +
22A GLU* 3.1 56.4 + - - +
98A ALA* 5.1 6.3 + - - +
100A VAL 5.1 7.9 + - - -
101A ASP 5.4 4.2 + - - -
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Residues in contact with ALA 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 ALA 3.1 17.4 + - - +
16A ALA* 3.7 6.1 - - - +
18A GLN* 1.3 75.4 - - - +
20A LEU* 1.3 54.2 + - - +
22A GLU* 3.3 4.4 + - - -
23A ARG* 2.7 67.3 + - - +
24A GLY 3.5 3.1 + - - +
28A PRO* 3.9 13.7 - - + -
33A VAL* 4.7 7.0 - - + -
55A MET* 4.6 0.7 - - + -
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Residues in contact with LEU 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 ALA 2.9 17.5 + - - +
17A THR 3.6 2.7 - - - +
18A GLN 3.3 0.2 - - - -
19A ALA* 1.3 76.7 - - - +
21A LEU* 1.3 60.3 + - - +
24A GLY* 3.0 33.6 + - - -
25A ALA* 3.7 26.7 - - + -
55A MET* 4.1 11.8 - - + +
58A ALA* 3.7 8.1 - - + -
59A PHE* 3.4 45.1 - - + +
62A LEU* 3.7 16.4 - - + -
105A PRO* 4.3 2.7 - - + -
108A ALA* 3.5 6.1 - - - +
109A THR* 3.5 28.0 - - + +
120A PHE* 5.0 0.4 - - + -
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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 THR* 2.9 21.2 + - - +
18A GLN* 3.4 27.6 + - - +
20A LEU* 1.3 75.1 - - - +
22A GLU* 1.3 62.1 + - + +
62A LEU* 3.7 23.3 - - + -
98A ALA* 6.0 2.5 - - + -
100A VAL 5.8 1.6 - - - +
101A ASP 5.8 1.1 - - - +
103A GLY* 3.2 45.8 - - - +
104A CYS 3.4 20.5 - - - +
105A PRO* 3.5 8.7 - - + -
108A ALA* 3.3 16.1 - - - +
160A ARG* 3.8 16.3 + - - +
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Residues in contact with GLU 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 GLN* 3.1 41.1 + - - +
19A ALA* 4.0 3.9 - - - +
20A LEU 3.2 0.6 - - - -
21A LEU* 1.3 83.7 - - + +
23A ARG* 1.3 71.7 + - + +
24A GLY 3.8 0.4 - - - -
98A ALA* 4.1 27.6 - - + +
108A ALA* 4.3 6.2 - - - +
160A ARG* 5.6 6.4 + - - +
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Residues in contact with ARG 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 ALA* 2.7 31.2 + - - +
22A GLU* 1.3 88.9 + - + +
24A GLY* 1.3 61.4 + - - +
27A GLU* 4.0 41.0 - - - +
28A PRO* 3.6 32.3 - - + +
32A GLU* 2.9 44.3 + - - +
108A ALA* 4.6 3.1 - - - +
112A GLU* 4.3 6.6 - - - +
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Residues in contact with GLY 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 LEU* 3.0 30.2 + - - -
22A GLU 3.8 0.4 - - - -
23A ARG* 1.3 79.6 - - - +
25A ALA* 1.3 61.1 + - - -
26A VAL 3.6 0.2 - - - -
28A PRO* 3.3 21.9 - - - +
55A MET* 3.5 0.5 - - - +
108A ALA* 3.5 21.9 - - - +
109A THR* 3.9 5.2 - - - -
112A GLU* 3.7 3.8 - - - -
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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