Contacts of the helix formed by residues 6 - 25 (chain A) in PDB entry 3D77
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 PRO 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TRP* 3.3 14.5 - - + +
5A VAL* 1.3 93.9 - - + +
7A PRO* 1.3 74.3 - - + +
8A GLU* 3.2 32.5 - - + +
9A VAL* 3.1 34.8 - - + +
10A PHE* 3.4 2.7 - - - -
73A LEU 5.5 4.5 - - - +
75A PRO* 6.1 1.3 - - + -
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Residues in contact with PRO 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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5A VAL 4.5 0.7 - - - +
6A PRO* 1.3 89.3 - - + +
8A GLU* 1.3 65.0 + - - +
10A PHE* 3.0 29.7 + - + +
11A ASP* 4.0 5.2 + - - +
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Residues in contact with GLU 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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6A PRO* 3.2 33.0 - - + +
7A PRO* 1.3 86.5 - - - +
9A VAL* 1.3 64.5 + - + +
11A ASP* 4.5 1.4 + - - +
12A LEU* 3.1 30.7 + - + +
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Residues in contact with VAL 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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4A TRP* 6.5 0.2 - - + -
5A VAL* 2.8 39.3 - - + -
6A PRO* 3.1 26.5 - - + +
8A GLU* 1.3 79.3 - - + +
10A PHE* 1.3 89.0 + - + +
11A ASP 3.2 0.7 - - - -
12A LEU* 3.0 11.3 + - - +
13A VAL* 2.9 29.9 + - + +
73A LEU 6.1 0.4 - - - +
119A ILE* 4.0 15.9 - - + -
121A NBB 5.9 5.4 - - + -
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Residues in contact with PHE 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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5A VAL* 3.4 35.9 - - + -
6A PRO 3.4 9.2 - - - -
7A PRO* 3.0 14.0 + - + +
9A VAL* 1.3 94.1 - - + +
11A ASP* 1.3 58.1 + - - +
13A VAL* 3.7 5.3 + - - +
14A ALA* 3.3 25.6 + - - +
17A LYS* 5.8 2.9 - - + -
117A PHE* 4.3 17.5 - + - -
119A ILE* 4.0 30.7 - - + -
126A EDO 4.5 4.5 + - - -
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Residues in contact with ASP 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 PRO 4.0 5.8 + - - +
8A GLU* 4.5 1.7 + - - +
9A VAL 3.2 0.2 - - - -
10A PHE* 1.3 78.9 - - - +
12A LEU* 1.3 63.5 + - - +
13A VAL 3.1 1.7 + - - -
14A ALA* 3.8 19.9 + - - +
15A GLU 5.2 0.5 + - - -
126A EDO 5.3 0.5 + - - -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.1 24.1 + - + +
9A VAL* 3.0 10.7 + - - +
11A ASP* 1.3 77.8 - - - +
13A VAL* 1.3 63.0 + - + +
14A ALA 3.8 0.2 + - - -
15A GLU* 4.9 4.3 + - - +
16A ASP* 4.7 7.4 + - - +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 2.9 24.5 + - + +
10A PHE* 4.0 4.9 - - - +
11A ASP 3.1 0.2 - - - -
12A LEU* 1.3 81.9 - - + +
14A ALA* 1.3 53.9 + - - +
15A GLU 3.3 2.9 - - - -
16A ASP* 3.1 7.5 + - - +
17A LYS* 2.7 30.3 + - + -
52A LEU* 4.0 10.3 - - + -
56A PHE* 3.2 46.0 - - + -
119A ILE* 3.7 31.9 - - + -
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Residues in contact with ALA 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 PHE 3.3 13.6 + - - +
11A ASP* 3.8 19.5 + - - +
12A LEU 3.5 1.6 - - - -
13A VAL* 1.3 76.7 - - - +
15A GLU* 1.3 63.4 + - - +
18A ALA* 3.0 12.6 + - - +
126A EDO 2.8 51.9 + - - +
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Residues in contact with GLU 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 ASP 5.2 0.4 + - - -
12A LEU 4.9 4.2 + - - +
13A VAL 3.3 0.6 - - - -
14A ALA* 1.3 78.9 - - - +
16A ASP* 1.3 63.6 + - - +
18A ALA* 3.4 2.3 + - - -
19A ARG* 3.0 17.2 + - + +
125A EDO 2.7 33.4 + - - +
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Residues in contact with ASP 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 LEU 4.7 9.2 - - - +
13A VAL* 3.1 9.1 + - - +
15A GLU* 1.3 83.6 - - - +
17A LYS* 1.3 60.6 + - - +
19A ARG* 2.9 31.4 + - - +
20A CYS* 2.8 35.5 + - - -
52A LEU* 4.0 9.0 - - + -
55A ALA* 3.6 30.2 - - + +
56A PHE* 4.9 5.2 - - + -
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Residues in contact with LYS 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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10A PHE* 5.8 3.2 - - + -
13A VAL* 2.7 28.7 + - + +
14A ALA 3.7 3.6 - - - +
16A ASP* 1.3 73.3 - - - +
18A ALA* 1.3 55.8 + - - +
20A CYS 3.8 0.2 - - - -
21A MET* 2.9 53.7 + - - +
28A GLN* 2.9 31.8 + - - +
31A ILE* 3.9 2.9 - - - +
48A TYR* 3.3 19.1 - - - +
52A LEU* 3.9 9.7 - - - +
119A ILE* 2.7 34.7 + - + +
126A EDO 3.6 26.7 - - - -
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Residues in contact with ALA 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 ALA 3.0 17.6 + - - +
15A GLU* 4.7 0.9 - - - -
17A LYS* 1.3 78.5 - - - +
19A ARG* 1.3 64.5 + - - +
21A MET* 3.9 6.9 - - - +
22A SER* 3.1 24.3 + - - -
125A EDO 3.7 23.5 + - - +
126A EDO 3.7 10.1 + - - +
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Residues in contact with ARG 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 GLU* 3.0 18.3 + - + +
16A ASP* 2.9 31.8 + - - +
18A ALA* 1.3 78.9 - - - +
20A CYS* 1.3 70.1 + - - +
22A SER* 3.2 3.4 + - - -
23A GLU* 2.9 72.3 + - + +
51A CYS* 3.5 12.1 + - - -
54A GLU* 4.9 5.9 + - - -
55A ALA* 4.0 11.5 - - - +
125A EDO 3.5 22.1 + - - +
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Residues in contact with CYS 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 ASP* 2.8 29.2 + - - +
17A LYS* 4.7 0.2 - - - -
19A ARG* 1.3 85.3 - - - +
21A MET* 1.3 61.9 + - - +
23A GLU* 4.5 0.2 - - - -
24A HIS* 3.1 30.6 + - - +
26A THR* 3.9 0.9 + - - -
48A TYR* 3.6 24.4 - - + +
51A CYS* 2.1 63.0 - - + -
52A LEU* 3.8 6.5 - - - -
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Residues in contact with MET 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 LYS* 2.9 48.5 + - - +
18A ALA* 3.9 6.3 - - - +
20A CYS* 1.3 77.0 - - - +
22A SER* 1.3 61.5 + - - +
25A GLY* 3.0 21.5 + - - -
26A THR* 3.2 37.5 + - - +
27A THR* 3.7 3.4 - - - +
28A GLN* 3.5 33.2 - - + +
31A ILE* 4.2 4.3 - - + -
48A TYR* 3.4 16.8 - - + -
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Residues in contact with SER 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 ALA 3.1 18.6 + - - -
19A ARG* 3.5 4.0 - - - -
21A MET* 1.3 77.5 - - - +
23A GLU* 1.3 66.0 + - - +
24A HIS 3.2 0.5 + - - -
25A GLY* 3.7 5.5 + - - -
125A EDO 4.0 13.0 + - - -
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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 ARG* 2.9 60.8 + - + +
21A MET 3.3 0.2 - - - -
22A SER* 1.3 78.4 - - - +
24A HIS* 1.3 90.2 + - + +
25A GLY 4.1 0.2 + - - -
51A CYS* 3.6 5.0 - - - -
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Residues in contact with HIS 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 CYS 3.1 25.1 + - - +
22A SER 3.2 0.2 - - - -
23A GLU* 1.3 106.7 + - + +
25A GLY* 1.3 60.7 + - - +
26A THR* 3.7 10.3 - - - +
43A PRO 4.9 0.4 - - - -
44A SER* 3.2 29.2 - - - +
47A CYS* 3.5 42.1 + - + +
48A TYR 4.2 1.3 - - - +
51A CYS* 3.8 17.7 - - + +
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Residues in contact with GLY 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 MET 3.0 7.7 + - - -
22A SER 3.7 4.4 + - - -
23A GLU 3.7 1.4 - - - -
24A HIS* 1.3 79.3 - - - +
26A THR* 1.3 63.8 + - - +
27A THR* 3.7 7.6 + - - +
30A GLN* 3.8 5.4 - - - +
44A SER* 3.9 6.3 - - - -
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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