Contacts of the helix formed by residues 2 - 17 (chain A) in PDB entry 1ECA
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 SER 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LEU* 1.3 74.6 + - - +
3A ALA* 1.3 65.8 + - - +
4A ASP* 2.8 23.9 + - - -
5A GLN* 3.1 13.6 + - - +
6A ILE* 3.0 26.9 + - - +
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Residues in contact with ALA 3 (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* 1.3 76.6 - - - +
4A ASP* 1.3 57.5 + - - +
6A ILE* 3.7 12.2 - - - +
7A SER* 2.9 31.7 + - - -
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Residues in contact with ASP 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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2A SER* 2.8 29.5 + - - -
3A ALA* 1.3 72.0 - - - +
5A GLN* 1.3 74.4 + - - +
7A SER* 2.7 22.6 + - - -
8A THR* 2.9 15.4 + - - -
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Residues in contact with GLN 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 LEU* 3.5 39.9 - - + +
2A SER* 3.7 10.6 + - - +
4A ASP* 1.3 93.0 + - - +
6A ILE* 1.3 65.9 + - - +
8A THR* 3.4 4.3 + - - -
9A VAL* 3.1 27.4 + - - +
119A ALA* 4.1 9.9 - - - +
120A ALA* 3.6 17.5 - - + +
123A ALA* 3.4 24.6 - - - +
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Residues in contact with ILE 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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1A LEU* 4.0 27.6 - - + +
2A SER 3.0 28.3 + - - +
3A ALA* 3.7 9.2 - - - +
4A ASP 3.2 0.2 - - - -
5A GLN* 1.3 78.1 - - - +
7A SER* 1.3 62.7 + - - +
9A VAL* 3.4 6.4 + - - +
10A GLN* 3.1 50.6 + - + +
73A LEU* 4.0 43.7 - - + +
74A PRO* 4.1 10.8 - - + -
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Residues in contact with SER 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 ALA 2.9 14.3 + - - -
4A ASP* 2.7 24.1 + - - -
6A ILE* 1.3 76.5 - - - +
8A THR* 1.3 60.3 + - - +
10A GLN* 3.9 11.4 - - - +
11A ALA* 3.0 30.0 + - - +
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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 ASP 2.9 13.2 + - - -
5A GLN* 3.4 9.8 - - - -
7A SER* 1.3 79.2 + - - +
9A VAL* 1.3 66.1 + - - +
11A ALA* 3.5 5.9 + - - +
12A SER* 3.0 21.3 + - - -
116A GLY 4.2 6.7 - - - +
117A ALA* 4.0 22.6 - - + +
120A ALA* 3.7 19.5 - - + -
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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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5A GLN 3.1 13.5 + - - +
6A ILE* 3.8 4.0 - - - +
7A SER 3.4 0.2 - - - -
8A THR* 1.3 80.3 - - - +
10A GLN* 1.3 54.6 + - - +
12A SER* 3.1 7.3 + - - -
13A PHE* 2.8 32.6 + - - +
70A ILE* 4.2 20.9 - - + -
73A LEU* 4.4 9.4 - - + -
120A ALA* 3.5 36.8 - - + +
121A TRP* 3.6 39.5 - - + +
124A THR* 3.6 10.8 - - - +
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Residues in contact with GLN 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 ILE* 3.1 41.2 + - + +
7A SER* 3.9 8.7 - - - +
8A THR 3.2 0.2 - - - -
9A VAL* 1.3 76.6 - - + +
11A ALA* 1.3 66.4 + - - +
13A PHE* 4.0 5.7 - - - +
14A ASP* 3.1 23.6 + - - +
70A ILE* 3.2 36.6 - - + +
71A GLY* 3.7 16.4 - - - +
73A LEU* 4.8 2.8 + - + +
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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
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7A SER 3.0 18.1 + - - +
8A THR* 3.6 6.7 - - - +
10A GLN* 1.3 77.2 - - - +
12A SER* 1.3 62.5 + - - +
14A ASP* 3.5 16.5 + - - +
15A LYS* 3.7 13.8 - - - +
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Residues in contact with SER 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 15.0 + - - -
9A VAL 3.4 8.1 - - - -
11A ALA* 1.3 77.7 - - - +
13A PHE* 1.3 62.9 + - - +
15A LYS* 3.4 29.3 + - - +
16A VAL* 4.1 2.6 + - - +
108A MET* 3.3 18.2 - - - +
112A THR* 5.0 3.5 + - - +
114A PHE* 5.1 0.9 - - - -
117A ALA* 4.1 14.9 - - - +
121A TRP* 2.9 25.5 + - - -
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Residues in contact with PHE 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 VAL 2.8 20.1 + - - +
10A GLN* 4.0 7.4 - - - +
12A SER* 1.3 71.0 + - - +
14A ASP* 1.3 65.5 + - - +
15A LYS 3.1 2.5 - - - -
16A VAL* 3.1 23.0 + - + +
17A LYS* 3.0 47.1 + - + +
23A ILE* 4.7 6.7 - - + -
63A VAL* 4.4 10.1 - - + -
66A PHE* 4.1 28.0 - + - -
67A SER* 3.7 35.4 - - - -
70A ILE* 4.4 16.4 - - + -
104A PHE* 4.5 8.3 - + - -
121A TRP* 4.0 25.1 - + + -
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Residues in contact with ASP 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 GLN 3.1 18.4 + - - +
11A ALA* 3.6 9.9 - - - +
12A SER 3.3 0.4 - - - -
13A PHE* 1.3 77.0 - - - +
15A LYS* 1.3 62.7 + - + +
16A VAL 3.4 0.5 + - - -
17A LYS* 3.0 45.0 + - - +
18A GLY 5.1 0.5 + - - -
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Residues in contact with LYS 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 3.7 13.2 - - - +
12A SER* 3.6 19.1 - - - +
13A PHE 3.1 0.8 - - - -
14A ASP* 1.3 79.7 - - + +
16A VAL* 1.3 64.6 + - + +
17A LYS 3.8 0.2 - - - -
18A GLY 5.3 0.7 + - - -
112A THR* 4.7 22.7 - - + +
113A ASP* 5.1 10.3 + - - +
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Residues in contact with VAL 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 SER 4.6 0.4 - - - +
13A PHE* 3.4 28.7 - - + +
15A LYS* 1.3 84.3 - - + +
17A LYS* 1.3 56.4 + - - +
18A GLY 3.1 5.8 - - - -
19A ASP* 3.0 27.0 + - - +
23A ILE* 3.9 11.1 - - + +
104A PHE* 5.4 0.2 - - + -
107A TYR* 3.8 29.2 - - + +
108A MET* 3.8 24.5 - - + -
111A HIS* 4.7 3.4 - - + -
112A THR* 3.6 31.2 - - + -
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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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13A PHE* 3.0 39.3 + - + +
14A ASP* 3.0 43.6 + - - +
15A LYS 3.8 0.2 - - - -
16A VAL* 1.3 79.3 - - - +
18A GLY* 1.3 61.6 + - - +
19A ASP 3.2 2.0 + - - -
20A PRO* 3.8 12.6 - - - +
23A ILE* 5.1 2.9 - - - -
63A VAL* 4.9 6.1 - - + +
67A SER* 5.0 7.2 - - - +
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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