Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 3A46
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 GLU 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 1.3 75.4 - - - +
4A GLY* 1.3 71.0 + - - +
5A PRO 3.3 1.1 - - - -
6A GLU* 2.9 27.7 + - - +
7A VAL* 3.2 9.0 + - - +
60A LYS* 4.1 6.7 - - - -
170A GLY 3.8 4.5 - - - +
172A GLY* 2.8 30.1 + - - -
174A TYR* 2.8 47.5 + - + -
175A LEU* 3.0 31.2 + - + +
20D 3DR 3.1 16.1 - - - +
21D G 3.3 17.3 - - - +
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Residues in contact with GLY 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 1.3 70.2 - - - +
5A PRO* 1.3 68.2 - - - +
7A VAL* 3.1 2.8 + - - +
8A ALA* 2.9 24.6 + - - +
59A GLY* 3.7 21.5 - - - +
60A LYS* 3.8 2.8 - - - +
138A ASP* 5.9 2.5 - - - -
140A LEU* 5.0 4.7 - - - -
170A GLY* 2.7 29.4 + - - -
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Residues in contact with PRO 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.6 4.7 - - + -
4A GLY* 1.3 87.6 - - - +
6A GLU* 1.3 63.8 + - - +
8A ALA* 3.4 1.4 + - - +
9A LEU* 3.0 25.5 + - - +
140A LEU* 4.2 16.4 - - + -
170A GLY 4.2 1.3 - - - +
174A TYR* 5.1 0.2 - - - +
175A LEU* 3.6 22.9 - - + -
210A THR* 3.6 28.7 - - + +
213A ALA* 3.8 16.4 - - + +
214A TYR* 3.7 28.9 - - + +
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 3.9 12.3 - - + -
3A GLU* 2.9 34.7 + - - +
5A PRO* 1.3 76.0 - - - +
7A VAL* 1.3 58.1 + - - +
9A LEU 3.5 0.2 + - - -
10A THR* 2.8 35.0 + - - +
82A PHE* 5.1 2.0 - - + -
174A TYR* 2.5 34.5 + - - -
213A ALA 5.2 0.5 - - - +
219A ILE* 3.6 21.9 - - + +
221A TYR* 4.1 21.3 - - + +
222A MET* 3.9 31.6 - - + +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.3 9.9 - - + -
3A GLU 3.2 10.5 + - - +
4A GLY 3.1 7.2 + - - +
6A GLU* 1.3 75.8 - - - +
8A ALA* 1.3 58.8 + - - +
10A THR* 3.7 5.8 - - - -
11A ALA 3.0 23.2 + - - -
57A THR* 3.4 27.4 - - + +
59A GLY 3.9 3.8 - - - +
60A LYS* 3.9 33.4 - - + +
62A LEU* 3.9 19.6 - - + +
82A PHE* 4.1 26.9 - - + -
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Residues in contact with ALA 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 GLY 2.9 15.7 + - - +
5A PRO 3.8 4.0 - - - +
7A VAL* 1.3 77.6 - - - +
9A LEU* 1.3 63.7 + - - +
11A ALA* 3.2 4.3 + - - +
12A ASP* 3.0 28.3 + - - +
57A THR* 3.8 19.9 + - - +
138A ASP* 5.9 0.4 - - - +
140A LEU* 3.9 22.7 - - + -
141A LYS* 4.8 9.0 - - + +
214A TYR* 4.2 6.5 - - + -
237A TYR* 5.3 2.9 - - + +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO 3.0 17.7 + - - +
6A GLU 3.9 2.9 - - - +
8A ALA* 1.3 76.0 - - - +
10A THR* 1.3 62.7 + - - +
12A ASP* 3.1 10.4 + - + +
13A ILE* 3.0 31.9 + - + +
214A TYR* 3.9 17.2 - - + +
216A SER 3.9 8.7 - - - +
222A MET* 3.8 27.1 - - + -
229A SER* 3.9 8.1 - - - +
232A ILE* 4.2 14.6 - - + -
233A GLY 4.6 1.3 - - - +
234A ARG* 3.5 54.5 - - - +
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Residues in contact with THR 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 GLU* 2.8 24.5 + - - +
7A VAL 3.7 4.3 - - - -
8A ALA 3.2 0.2 - - - -
9A LEU* 1.3 77.3 - - - +
11A ALA* 1.3 59.1 + - - +
13A ILE* 3.3 6.5 + - - +
14A LEU* 2.9 33.0 + - + +
62A LEU* 4.4 0.2 - - + -
82A PHE* 3.9 17.4 - - + -
88A TRP* 3.7 41.0 + - + +
222A MET* 3.5 22.2 - - - +
225A LEU* 4.2 9.2 - - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL 3.0 7.9 + - - +
8A ALA 3.5 4.0 - - - +
10A THR* 1.3 78.3 - - - +
12A ASP* 1.3 58.9 + - - +
14A LEU* 3.2 3.3 + - - +
15A GLU* 2.8 32.3 + - - +
55A VAL* 3.8 27.8 - - + +
56A ASP* 4.5 0.7 - - - -
57A THR* 3.3 33.7 - - + +
62A LEU* 3.8 9.4 - - + +
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.0 19.3 + - - +
9A LEU* 3.1 12.1 + - + +
11A ALA* 1.3 78.8 - - - +
13A ILE* 1.3 55.7 + - - +
15A GLU* 3.3 10.2 + - - +
16A LYS* 3.0 26.7 + - - +
214A TYR* 2.7 34.2 + - - -
232A ILE* 3.7 16.5 - - + +
235A LYS* 4.3 19.8 - - - +
237A TYR* 4.9 5.4 + - - -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.0 17.6 + - + +
10A THR* 3.7 6.5 - - - +
12A ASP* 1.3 73.8 - - - +
14A LEU* 1.3 67.5 + - + +
16A LYS* 3.0 2.8 + - - +
17A TYR* 3.0 52.8 + - + -
90A LEU* 5.5 1.8 - - + -
222A MET* 4.1 21.5 - - + -
225A LEU* 4.2 23.1 - - + -
228A GLU* 4.0 25.4 - - + -
229A SER* 4.1 16.2 - - - +
232A ILE* 4.1 24.7 - - + -
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Residues in contact with LEU 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 THR* 2.9 36.9 + - + +
11A ALA 3.2 4.7 + - - +
13A ILE* 1.3 78.2 - - + +
15A GLU* 1.3 58.6 + - - +
18A PHE* 2.8 61.3 + - + +
19A LYS 3.9 0.3 + - - -
55A VAL* 3.9 14.7 - - + +
62A LEU* 4.1 17.0 - - + -
64A PHE* 3.6 26.5 - - + -
88A TRP* 4.1 32.3 - - + -
89A SER 5.9 1.3 - - - +
90A LEU* 5.9 1.3 - - + -
108A ALA* 5.1 1.3 - - + -
225A LEU* 6.0 2.2 - - + -
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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 ALA 2.8 12.4 + - - +
12A ASP* 3.6 11.0 - - - +
13A ILE 3.1 0.2 - - - -
14A LEU* 1.3 74.8 - - - +
16A LYS* 1.3 66.3 + - - +
19A LYS* 3.0 67.6 + - + +
54A ASN* 3.7 9.4 + - - +
55A VAL* 3.3 48.2 + - + +
235A LYS* 6.2 0.3 - - - -
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Residues in contact with LYS 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 ASP 3.0 13.6 + - - +
13A ILE* 3.0 9.4 + - + +
15A GLU* 1.3 80.3 - - - +
17A TYR* 1.3 98.4 + - + +
19A LYS 4.9 1.2 + - - +
21A LYS* 5.9 0.5 + - - -
228A GLU 5.2 0.8 + - - -
231A LYS* 3.0 35.6 + - - +
232A ILE* 4.0 24.9 - - + +
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Residues in contact with TYR 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 ILE* 3.0 44.2 + - + +
16A LYS* 1.3 115.1 + - + +
18A PHE* 1.3 86.7 + + + +
19A LYS 3.9 0.9 - - - -
21A LYS* 3.8 21.4 + - - +
90A LEU* 4.0 21.5 - - + -
106A LEU* 4.8 6.9 - - + +
228A GLU* 2.3 33.9 + - + -
231A LYS* 4.1 6.1 - - - -
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Residues in contact with PHE 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 LEU* 2.8 47.9 + - + +
17A TYR* 1.3 87.5 - - + +
19A LYS* 1.3 67.1 + - - +
21A LYS* 3.1 21.5 + - + +
52A VAL* 3.3 16.8 - - + +
64A PHE* 5.2 6.7 - + + -
89A SER 5.7 0.2 - - - -
90A LEU* 3.6 24.7 - - + -
102A PHE* 3.6 42.6 - + + -
106A LEU* 3.6 25.8 - - + -
107A MET 3.4 22.4 - - - -
108A ALA* 3.5 17.3 - - + -
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Residues in contact with LYS 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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14A LEU 3.9 2.0 + - - -
15A GLU* 3.0 64.0 + - + +
16A LYS 5.5 0.9 - - - +
17A TYR 5.1 0.7 - - - +
18A PHE* 1.3 79.1 - - - +
20A GLY* 1.3 63.2 + - - +
21A LYS* 3.1 11.6 + - - +
52A VAL* 3.8 9.8 - - + +
53A SER* 3.3 27.3 + - - +
54A ASN* 4.4 7.0 - - - +
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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
------------------------------------------------------------
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