Contacts of the helix formed by residues 2 - 19 (chain A) in PDB entry 1DT7
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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET* 2.6 28.1 + - + +
1A SER* 1.3 71.4 - - - +
3A LEU* 1.3 63.9 + - - +
4A GLU* 3.1 4.1 + - - +
5A LYS* 2.4 66.6 + - + +
6A ALA* 3.4 4.5 + - - +
9B ALA* 4.2 11.6 - - + +
12B ASP* 3.5 30.8 - - - +
13B VAL* 3.7 8.7 - - + +
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Residues in contact with LEU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 2.8 4.9 + - - +
2A GLU* 1.3 79.2 - - - +
4A GLU* 1.3 62.8 + - - +
6A ALA* 3.2 5.1 + - - +
7A MET* 3.1 41.3 + - + +
9B ALA 6.1 0.4 - - - -
10B LEU* 4.4 11.2 - - + -
13B VAL* 3.8 18.4 - - + +
35B LEU* 5.0 9.9 - - + -
39B GLU* 3.3 25.8 - - - +
40B LEU* 4.1 24.5 - - + -
43B PHE* 4.9 3.6 - - + -
73B PHE* 5.2 4.0 - - + -
77B VAL* 3.8 28.0 - - + -
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Residues in contact with GLU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 4.1 5.0 + - - +
2A GLU* 3.1 2.0 - - - -
3A LEU* 1.3 80.4 - - - +
5A LYS* 1.3 62.5 + - - +
6A ALA 3.4 0.2 + - - -
7A MET* 3.5 2.1 + - - +
8A VAL* 3.2 28.3 + - + +
43B PHE* 3.5 51.2 - - + +
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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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2A GLU* 2.4 52.4 + - + +
4A GLU* 1.3 81.5 - - - +
6A ALA* 1.3 67.6 + - - +
8A VAL* 3.5 6.1 + - - +
9A ALA* 3.1 24.3 + - - +
9B ALA* 4.3 12.8 - - - -
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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 GLU 3.4 7.8 + - - +
3A LEU* 3.2 12.3 + - - +
4A GLU 3.2 0.6 - - - -
5A LYS* 1.3 82.7 - - - +
7A MET* 1.3 66.4 + - - +
9A ALA* 3.4 5.3 + - - +
10A LEU* 3.1 24.6 + - - +
6B ALA* 4.8 7.1 - - - +
9B ALA* 4.2 21.8 - - + -
10B LEU* 3.9 28.8 - - + +
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Residues in contact with MET 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 LEU* 3.1 38.0 + - + +
4A GLU 4.1 4.0 - - - +
5A LYS 3.3 0.2 - - - -
6A ALA* 1.3 77.0 - - + +
8A VAL* 1.3 63.1 + - - +
10A LEU* 3.4 3.8 + - - +
11A ILE* 3.3 28.5 + - - +
10B LEU* 5.7 1.8 - - + -
43B PHE* 3.4 31.4 - - + -
77B VAL* 3.6 19.1 - - + +
80B VAL* 4.0 17.3 - - + +
81B THR* 3.0 48.8 - - + +
84B CYS* 4.5 11.2 - - - -
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Residues in contact with VAL 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 GLU* 3.2 25.9 + - + +
5A LYS* 3.9 7.6 - - - +
6A ALA 3.3 0.4 - - - -
7A MET* 1.3 81.2 - - + +
9A ALA* 1.3 56.3 + - - +
11A ILE* 3.5 3.3 + - - +
12A ASP* 2.9 41.0 + - - +
43B PHE* 5.9 0.4 - - + -
84B CYS* 5.0 8.7 - - - -
88B PHE* 3.7 42.8 - - + -
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Residues in contact with ALA 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 3.1 17.3 + - - +
6A ALA* 3.9 5.2 - - - +
7A MET 3.2 0.2 - - - -
8A VAL* 1.3 74.6 - - - +
10A LEU* 1.3 68.6 + - - +
12A ASP* 3.0 20.5 + - - +
13A VAL* 3.3 12.8 + - - +
2B GLU* 4.1 9.0 - - - +
3B LEU* 6.1 0.2 - - - -
5B LYS* 4.3 21.5 - - - -
6B ALA* 4.2 18.7 - - + +
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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
----------------------------------------------------------
6A ALA 3.1 13.2 + - - +
7A MET* 3.7 8.3 - - - +
8A VAL 3.3 0.2 - - - -
9A ALA* 1.3 81.0 - - - +
11A ILE* 1.3 61.7 + - - +
13A VAL* 3.7 7.3 + - + +
14A PHE* 3.6 15.4 + - - +
73A PHE* 4.9 4.9 - - + -
74A MET* 3.3 38.8 - - + -
77A VAL* 3.6 39.9 - - + -
81A THR* 5.9 0.4 - - - +
3B LEU* 4.4 6.3 - - + -
6B ALA* 3.9 25.4 - - + +
7B MET* 5.4 1.3 - - + +
10B LEU* 6.0 6.1 - - + -
81B THR* 4.6 0.7 - - + +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET 3.3 16.9 + - - +
8A VAL 3.8 4.0 - - - +
9A ALA 3.2 0.2 - - - -
10A LEU* 1.3 77.1 - - - +
12A ASP* 1.3 66.3 + - - +
14A PHE* 3.2 10.2 + - + +
15A HIS* 3.2 18.2 + - - +
70A PHE* 5.7 2.7 - - + -
74A MET* 4.8 7.2 - - - -
81B THR* 3.8 21.5 - - + +
84B CYS* 4.0 8.7 - - + -
85B HIS* 3.5 49.1 - - + +
88B PHE* 4.0 20.4 - - + -
90B HIS* 3.9 25.8 - - + +
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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 VAL* 2.9 31.8 + - - +
9A ALA* 3.0 11.9 + - - +
11A ILE* 1.3 76.7 - - - +
13A VAL* 1.3 54.1 + - - +
15A HIS* 3.2 7.8 + - - +
16A GLN* 2.4 39.4 + - - +
2B GLU* 3.5 17.0 - - - +
88B PHE* 3.4 23.1 - - - -
90B HIS* 5.0 3.0 + - - +
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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 ALA 3.3 7.8 + - - +
10A LEU* 4.2 9.2 - - + +
12A ASP* 1.3 78.9 - - - +
14A PHE* 1.3 69.3 + - - +
16A GLN* 3.0 25.2 + - + +
17A TYR* 3.7 3.5 + - - -
35A LEU* 4.4 4.9 - - + -
39A GLU* 3.1 44.9 - - - +
73A PHE* 5.0 6.7 - - + -
1B SER 3.6 22.0 - - - +
2B GLU* 3.7 17.6 + - + +
3B LEU* 3.8 23.8 - - + +
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Residues in contact with PHE 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 3.6 9.7 + - - +
11A ILE* 3.2 13.9 + - + +
12A ASP 3.2 0.6 - - - -
13A VAL* 1.3 86.3 - - - +
15A HIS* 1.3 65.2 + - + +
16A GLN 3.3 0.2 + - - -
17A TYR* 3.4 3.6 + - - +
18A SER* 3.0 38.4 + - - -
24A LYS 3.9 9.2 - - - -
25A HIS 5.1 0.9 - - - -
27A LEU* 3.2 39.3 - - + -
35A LEU* 5.9 0.9 - - - -
70A PHE* 3.2 44.6 - + + -
73A PHE* 3.6 34.1 - + + -
74A MET* 5.7 3.8 - - + -
85B HIS* 5.4 9.0 - + - -
90B HIS* 5.2 6.3 - + - -
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Residues in contact with HIS 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 ILE 3.2 3.7 + - - +
12A ASP* 3.2 6.1 + - - +
13A VAL 3.1 1.2 - - - -
14A PHE* 1.3 83.0 - + - +
16A GLN* 1.3 76.0 + - - +
18A SER* 3.6 11.7 - - - -
19A GLY* 3.2 24.2 + - - -
24A LYS* 4.9 16.2 - - + +
90B HIS* 3.3 55.6 + + + +
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Residues in contact with GLN 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* 2.4 42.2 + - - +
13A VAL* 3.0 16.1 + - + +
15A HIS* 1.3 87.8 + - - +
17A TYR* 1.3 72.7 + - + +
19A GLY 4.6 0.3 - - - -
20A ARG* 3.9 13.9 + - - +
39A GLU* 5.0 0.7 - - - +
0B MET* 3.4 30.6 - - - +
1B SER 5.2 2.0 - - - +
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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 VAL 4.0 2.0 - - - +
14A PHE* 3.4 5.1 + - - +
15A HIS 3.2 0.2 - - - -
16A GLN* 1.3 87.4 - - + +
18A SER* 1.3 67.7 + - - +
19A GLY 3.2 1.6 - - - -
20A ARG* 2.9 33.8 + - - +
21A GLU* 3.9 1.7 + - - +
27A LEU* 5.0 11.1 - - + +
31A GLU* 4.6 6.1 - - + +
34A GLU* 3.0 35.4 - - + -
35A LEU* 3.4 27.1 - - + -
38A ASN* 2.7 20.9 + - + -
39A GLU* 2.7 63.6 + - + +
114A CA 4.0 2.3 - - - -
1B SER 6.0 0.7 - - - -
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Residues in contact with SER 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 PHE* 3.0 49.2 + - - -
15A HIS* 3.6 10.4 - - - -
17A TYR* 1.3 77.7 - - - +
19A GLY* 1.3 61.6 + - - +
20A ARG 3.2 0.3 + - - -
21A GLU 3.0 17.0 + - - +
24A LYS* 3.3 27.3 + - - +
27A LEU* 3.9 4.6 - - - +
114A CA 2.8 25.0 - - - -
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Residues in contact with GLY 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 HIS* 3.2 20.1 + - - -
16A GLN 4.6 0.9 - - - -
17A TYR 3.2 0.4 - - - -
18A SER* 1.3 82.3 + - - +
20A ARG* 1.3 66.3 + - - +
21A GLU 3.3 5.8 - - - +
24A LYS* 4.5 14.6 - - - -
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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