Contacts of the helix formed by residues 7 - 21 (chain A) in PDB entry 5HOO
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 ASN 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL 3.9 1.0 + - - -
6A PRO* 1.3 72.0 - - - +
8A LYS* 1.3 58.0 + - - +
9A GLU* 2.9 24.7 + - - +
10A GLN* 2.6 56.9 + - - +
11A THR* 2.7 31.1 + - - -
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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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7A ASN* 1.3 75.7 - - - +
9A GLU* 1.3 71.5 + - - +
11A THR* 3.4 6.9 + - - -
12A ARG* 3.1 58.5 + - - +
62A ASP* 3.0 32.5 + - - -
20C A 4.3 5.7 + - - -
21C T 3.8 16.6 - - - +
39D T 4.3 5.9 + - - -
40D C 3.5 33.9 + - - +
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Residues in contact with GLU 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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7A ASN* 2.9 29.7 + - - +
8A LYS* 1.3 80.3 + - - +
10A GLN* 1.3 59.9 + - + +
12A ARG* 3.1 15.3 + - - +
13A THR* 3.0 30.3 + - - -
60A VAL* 3.6 26.6 - - + +
61A ASP* 4.4 16.4 - - - +
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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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4A PHE* 3.7 26.9 - - + -
5A VAL 4.5 0.7 - - - +
6A PRO* 3.5 15.4 - - + +
7A ASN* 2.6 52.8 + - - +
9A GLU* 1.3 74.1 - - + +
11A THR* 1.3 60.4 + - - +
13A THR* 3.5 3.5 + - - -
14A VAL* 3.2 27.6 + - - +
36A PHE* 6.5 0.2 - - - -
13B THR* 3.4 37.3 + - + +
16B ILE* 4.6 7.7 - - - +
58B PHE 5.2 1.8 + - - -
60B VAL* 4.6 7.9 - - - +
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Residues in contact with THR 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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6A PRO* 3.9 19.0 + - - +
7A ASN 2.7 22.6 + - - -
8A LYS* 3.4 7.0 - - - -
9A GLU 3.2 0.4 - - - -
10A GLN* 1.3 77.7 - - - +
12A ARG* 1.3 63.5 + - + +
14A VAL* 3.3 9.9 + - - +
15A LEU* 3.2 26.2 + - + +
32A LEU* 4.5 19.0 - - + +
36A PHE* 5.9 1.3 - - - -
40A VAL* 5.5 2.3 - - + +
41A PRO* 4.0 32.7 - - + +
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Residues in contact with ARG 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* 3.1 49.4 + - - +
9A GLU* 3.1 15.0 + - - +
11A THR* 1.3 75.8 - - + +
13A THR* 1.3 64.3 + - - +
15A LEU* 3.3 13.0 + - + +
16A ILE* 3.1 24.3 + - - +
49A TRP* 3.1 41.4 - - + +
53A PHE* 4.0 2.4 - - + -
60A VAL* 3.2 40.4 + - + +
61A ASP 4.7 0.2 - - - -
62A ASP* 2.8 30.5 + - - +
20C A 3.2 10.3 + - - -
21C T 2.9 28.9 + - - -
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Residues in contact with THR 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 GLU 3.0 14.5 + - - -
10A GLN* 3.6 11.6 - - - -
11A THR 3.3 0.2 - - - -
12A ARG* 1.3 73.0 - - - +
14A VAL* 1.3 60.3 + - - +
16A ILE* 3.0 16.7 + - + +
17A PHE* 2.9 24.6 + - - +
60A VAL* 4.2 5.4 - - - +
4B PHE* 6.2 1.6 - - + -
10B GLN* 3.4 62.0 + - + +
13B THR* 4.4 6.1 - - + -
14B VAL* 4.1 11.0 - - + -
36B PHE* 5.7 2.1 - - + -
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Residues in contact with VAL 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 3.2 14.6 + - - +
11A THR* 3.3 9.6 + - - +
13A THR* 1.3 76.4 - - - +
15A LEU* 1.3 58.7 + - + +
17A PHE* 3.1 8.0 + - - +
18A CYS* 2.8 31.9 + - - -
32A LEU* 4.0 13.9 - - + -
36A PHE* 4.9 7.0 - - + -
13B THR* 4.1 13.2 - - + -
14B VAL* 4.8 5.4 - - + -
17B PHE* 3.4 64.4 - - + -
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Residues in contact with LEU 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 THR* 3.2 22.7 + - + +
12A ARG* 3.5 15.9 - - + +
13A THR 3.2 0.6 - - - -
14A VAL* 1.3 74.1 - - + +
16A ILE* 1.3 58.6 + - - +
18A CYS* 3.9 3.5 - - - +
19A PHE* 3.0 30.1 + - - +
28A SER* 4.5 10.3 - - - -
32A LEU* 4.2 15.0 - - + -
41A PRO* 6.2 1.8 - - + -
45A THR 5.5 0.2 - - - -
46A CYS* 3.8 39.0 - - + -
49A TRP* 4.1 30.7 - - + -
50A PHE* 3.7 15.1 - - + -
53A PHE* 3.7 14.8 - - + -
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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 ARG 3.1 7.6 + - - +
13A THR* 3.0 13.9 + - + +
15A LEU* 1.3 74.1 - - - +
17A PHE* 1.3 63.4 + - - +
19A PHE* 3.3 2.8 + - - +
20A HIS* 3.0 40.9 + - + +
53A PHE* 3.4 32.1 - - + -
58A PHE* 4.0 23.8 - - + +
60A VAL* 3.8 28.3 - - + -
4B PHE* 3.4 42.4 - - + -
10B GLN* 4.6 2.7 - - - +
36B PHE* 4.4 2.9 - - + -
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Residues in contact with PHE 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 THR 2.9 10.6 + - - +
14A VAL* 3.2 9.2 - - - +
16A ILE* 1.3 78.9 - - - +
18A CYS* 1.3 62.8 + - - +
20A HIS* 3.2 3.1 + - - +
21A LEU* 3.0 46.6 + - + +
14B VAL* 3.5 39.9 - - + -
17B PHE* 4.2 22.9 - + - -
18B CYS* 4.2 6.7 - - - -
31B MET* 3.8 37.0 - - + -
32B LEU* 4.1 9.0 - - + -
35B ALA* 3.8 18.2 - - + -
36B PHE* 3.7 27.8 - + + -
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Residues in contact with CYS 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 VAL* 2.8 35.6 + - - +
15A LEU* 3.9 6.3 - - - +
17A PHE* 1.3 73.6 - - - +
19A PHE* 1.3 63.7 + - - +
21A LEU* 3.0 19.8 + - - +
22A LYS 3.4 0.2 + - - -
23A LYS* 3.1 26.4 + - + +
28A SER* 3.4 38.4 - - - +
31A MET* 4.0 25.6 - - - -
32A LEU* 6.1 0.9 - - - -
50A PHE* 4.7 0.7 - - + -
17B PHE* 4.3 4.9 - - - -
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Residues in contact with PHE 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 LEU 3.0 18.4 + - - +
16A ILE 3.5 4.5 - - - +
18A CYS* 1.3 75.4 - - - +
20A HIS* 1.3 71.2 + + - +
22A LYS* 2.9 26.2 + - - +
23A LYS 4.0 2.6 + - - +
50A PHE* 3.9 38.0 - + + -
53A PHE* 3.2 43.5 - + + -
54A LYS* 3.8 35.4 - - + -
58A PHE* 4.3 7.4 - + - -
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Residues in contact with HIS 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* 3.0 36.4 + - + +
17A PHE 3.7 4.9 - - - +
19A PHE* 1.3 82.0 - + - +
21A LEU* 1.3 57.5 + - - +
22A LYS* 3.1 32.8 + - - +
58A PHE* 3.9 16.7 - + - -
3B SER* 3.6 21.3 - - - -
4B PHE* 3.8 31.1 - + + +
34B GLU* 4.0 4.7 - - - +
35B ALA* 3.5 40.7 + - + +
36B PHE* 4.0 8.6 - + + -
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Residues in contact with LEU 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 PHE* 3.0 45.4 + - + +
18A CYS* 3.0 14.1 + - - +
20A HIS* 1.3 74.2 - - - +
22A LYS* 1.3 71.7 + - - +
23A LYS* 3.2 21.1 + - + +
31A MET* 5.4 7.0 - - + -
31B MET* 3.4 43.1 - - + +
34B GLU* 3.9 19.1 - - + +
35B ALA* 3.8 15.3 - - + +
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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