Contacts of the helix formed by residues 3 - 20 (chain A) in PDB entry 4I6U
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 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 3.9 0.6 + - - -
2A GLU* 1.3 72.8 - - - +
4A PHE* 1.3 63.2 + - - +
5A LEU* 4.2 0.2 - - - +
6A LEU* 3.0 33.6 + - - +
7A SER* 3.0 22.0 + - - -
44A ASN* 4.6 2.1 - - - +
103A PEG 5.7 1.2 + - - -
76B LEU* 4.9 3.0 - - - +
50D ILE* 5.1 0.2 - - - +
51D LYS* 4.1 25.3 - - - +
54D GLU* 2.6 27.2 + - - +
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Residues in contact with PHE 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 GLU 3.3 6.2 + - - +
3A SER* 1.3 71.4 - - - +
5A LEU* 1.3 65.8 + - - +
7A SER* 2.7 24.8 + - - -
8A LYS* 3.0 48.1 + - + +
75A ILE* 4.1 22.0 - - + -
78A HIS* 3.7 26.7 - + + -
104A PEG 3.7 41.3 - - - +
54D GLU* 3.6 9.7 + - - +
64D ASP* 3.6 24.2 - - - -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.4 0.4 - - - +
4A PHE* 1.3 78.4 - - + +
6A LEU* 1.3 58.9 + - - +
8A LYS* 3.2 3.6 + - + +
9A VAL* 2.8 45.6 + - + +
71A LEU* 4.3 7.2 - - + -
75A ILE* 4.5 12.3 - - + -
50D ILE* 3.7 31.9 - - + +
53D LEU* 4.5 7.0 - - + -
54D GLU* 2.9 38.7 + - + +
57D MET* 4.4 8.3 - - - -
64D ASP* 4.9 9.4 - - - +
68D PHE* 3.7 39.0 - - + -
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Residues in contact with LEU 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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3A SER* 3.0 24.6 + - - +
5A LEU* 1.3 77.3 - - - +
7A SER* 1.3 57.4 + - - +
9A VAL* 3.4 1.7 + - + -
10A SER* 2.8 36.7 + - - +
44A ASN* 3.9 8.1 - - - +
46A ARG 3.6 28.5 - - - +
47A ASN* 4.0 18.4 - - - +
48A LEU* 3.8 24.2 - - + -
101A NA 3.7 11.4 - - - -
103A PEG 4.0 21.3 - - - +
50D ILE* 3.8 15.2 - - + +
51D LYS* 4.2 11.7 - - + -
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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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2A GLU* 6.2 0.2 - - - -
3A SER 3.0 13.7 + - - -
4A PHE* 2.7 25.5 + - - -
6A LEU* 1.3 76.3 - - - +
8A LYS* 1.3 64.5 + - - +
10A SER* 3.6 3.1 - - - -
11A PHE* 3.0 27.5 + - - +
44A ASN* 3.4 28.4 + - - -
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Residues in contact with LYS 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 PHE* 3.0 46.9 + - + +
5A LEU* 3.2 7.4 + - - +
7A SER* 1.3 79.8 + - - +
9A VAL* 1.3 64.8 + - - +
11A PHE* 3.4 10.0 + - + +
12A VAL* 2.9 28.4 + - - +
71A LEU* 3.9 17.0 - - + -
74A GLU* 4.0 26.9 + - + +
75A ILE* 4.2 6.3 - - + -
78A HIS* 3.1 44.1 + - - +
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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 LEU* 2.8 40.3 + - + +
6A LEU* 3.8 7.0 - - + +
8A LYS* 1.3 71.2 - - - +
10A SER* 1.3 64.3 + - - +
12A VAL* 3.2 4.0 + - - +
13A ILE* 3.0 39.0 + - + +
48A LEU* 4.6 8.3 - - + -
53A LEU* 4.2 10.3 - - + -
67A PHE* 4.1 14.4 - - + -
68A PHE* 6.2 0.4 - - + -
71A LEU* 4.1 18.4 - - + -
50D ILE* 4.2 29.4 - - + -
68D PHE* 5.9 0.4 - - + -
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Residues in contact with SER 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 LEU* 2.8 24.4 + - - +
7A SER* 3.6 7.6 - - - -
9A VAL* 1.3 76.3 - - - +
11A PHE* 1.3 64.0 + - - +
13A ILE* 3.4 4.5 + - - +
14A LYS* 3.1 22.7 + - - +
41A ILE* 2.9 42.7 + - - +
42A GLU* 4.6 10.7 - - - +
44A ASN* 4.2 5.3 + - - -
101A NA 3.1 11.1 - - - -
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Residues in contact with PHE 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 15.4 + - - +
8A LYS* 3.7 12.8 - - + +
10A SER* 1.3 79.8 - - - +
12A VAL* 1.3 59.8 + - + +
14A LYS* 3.2 17.9 + - + +
15A LYS* 2.9 48.1 + - + +
74A GLU* 3.2 40.8 - - + -
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Residues in contact with VAL 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 LYS 2.9 21.5 + - - +
9A VAL 3.2 3.3 + - - +
11A PHE* 1.3 74.2 - - - +
13A ILE* 1.3 63.8 + - - +
15A LYS* 3.3 7.1 + - + +
16A ILE* 3.0 37.3 + - + +
67A PHE* 3.6 29.4 - - + +
70A MET* 4.0 20.0 - - + +
71A LEU* 3.9 20.2 - - + -
74A GLU* 3.7 28.7 - - + -
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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 VAL* 3.0 36.5 + - + +
10A SER* 3.6 6.1 - - - +
11A PHE 3.3 0.4 - - - -
12A VAL* 1.3 74.9 - - - +
14A LYS* 1.3 59.9 + - - +
16A ILE* 4.0 1.6 - - - +
17A ARG* 2.9 29.6 + - - +
27A LEU* 3.8 26.9 - - + -
38A ILE* 5.9 1.1 - - + -
41A ILE* 4.1 23.3 - - + -
42A GLU* 4.2 11.0 - - + +
48A LEU* 4.5 2.7 - - + -
53A LEU* 4.2 7.4 - - + -
56A ILE* 3.9 32.3 - - + -
60A LEU* 4.2 6.4 - - + +
67A PHE* 3.8 18.2 - - + -
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Residues in contact with LYS 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 SER 3.1 12.4 + - - +
11A PHE* 3.6 21.3 - - + +
13A ILE* 1.3 75.9 - - - +
15A LYS* 1.3 58.6 + - - +
17A ARG* 3.3 16.2 + - - +
18A LEU* 3.0 48.1 + - + +
42A GLU* 3.4 41.3 + - + +
61C GLU* 4.8 14.6 + - - -
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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 PHE* 2.9 42.3 + - + +
12A VAL* 3.7 6.7 - - + +
13A ILE 3.3 0.2 - - - -
14A LYS* 1.3 78.5 - - - +
16A ILE* 1.3 58.1 + - - +
18A LEU* 3.4 6.2 + - - +
19A GLU* 3.0 58.1 + - + +
70A MET* 4.2 18.8 - - + -
74A GLU* 3.2 24.8 + - + +
77A LYS* 4.0 10.1 - - - +
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Residues in contact with ILE 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 VAL* 3.0 37.8 + - + +
13A ILE 4.0 2.5 - - - +
15A LYS* 1.3 73.5 - - - +
17A ARG* 1.3 66.0 + - - +
19A GLU* 3.2 11.0 + - + +
20A LYS* 2.9 40.3 + - + +
60A LEU* 3.8 27.1 - - + +
62A VAL* 4.5 18.8 - - + -
67A PHE* 3.8 20.2 - - + -
70A MET* 3.7 32.8 - - + -
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Residues in contact with ARG 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 2.9 19.3 + - - +
14A LYS* 3.3 21.3 + - - +
16A ILE* 1.3 74.2 - - - +
18A LEU* 1.3 78.3 + - - +
20A LYS* 3.2 10.9 + - - -
22A MET* 2.9 68.4 + - + +
23A THR* 3.6 18.5 - - - +
24A GLN* 3.6 28.0 - - - +
27A LEU* 4.1 16.2 - - + -
42A GLU* 2.7 42.0 + - - +
60A LEU* 3.6 14.9 - - + +
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Residues in contact with LEU 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 LYS* 3.0 45.2 + - + +
15A LYS* 3.9 5.6 - - - +
17A ARG* 1.3 98.4 - - - +
19A GLU* 1.3 63.5 + - + +
20A LYS 3.1 1.3 - - - -
21A GLY* 3.0 14.5 + - - +
22A MET 4.3 4.9 - - - +
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Residues in contact with GLU 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 LYS* 3.0 51.9 + - + +
16A ILE* 3.2 11.0 + - + +
18A LEU* 1.3 76.3 - - + +
20A LYS* 1.3 64.0 + - + +
21A GLY 3.5 0.5 + - - -
70A MET* 4.1 15.4 - - - +
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Residues in contact with LYS 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 ILE* 2.9 32.7 + - + +
17A ARG 3.2 5.4 + - - +
18A LEU 3.1 0.6 - - - -
19A GLU* 1.3 81.9 - - - +
21A GLY* 1.3 61.2 + - - +
22A MET* 3.3 24.0 + - - +
60A LEU* 2.8 29.6 + - + +
61A GLU* 3.1 23.4 + - - +
62A VAL* 5.0 3.2 - - - +
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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
------------------------------------------------------------
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