Contacts of the helix formed by residues 4 - 20 (chain A) in PDB entry 8CHO
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 PRO 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN 4.4 2.5 - - - +
3A THR* 1.3 88.0 - - + +
5A GLU* 1.3 54.3 + - - +
7A MET* 3.4 6.7 + - + +
8A THR* 2.7 39.0 + - - +
73A ALA* 3.9 34.8 - - + +
74A VAL* 5.2 2.5 - - - -
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Residues in contact with GLU 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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3A THR* 3.0 11.4 + - - +
4A PRO* 1.3 81.1 - - - +
6A HIS* 1.3 58.0 + - - +
8A THR* 3.9 5.5 - - - -
9A ALA* 3.0 27.2 + - + +
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Residues in contact with HIS 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 MET 4.4 8.5 - - - +
2A ASN* 3.5 20.9 - - - -
3A THR* 3.1 23.9 + - - +
5A GLU* 1.3 75.0 - - - +
7A MET* 1.3 68.6 + - + +
9A ALA* 3.1 8.7 + - - +
10A VAL* 2.9 44.7 + - + +
13A ARG* 4.6 14.3 + - - -
103A PHE* 4.5 1.6 - + - -
106A ALA 5.4 0.9 - - - -
107A GLY* 2.8 33.8 + - - -
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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
----------------------------------------------------------
2A ASN* 4.3 15.0 - - + +
3A THR 3.1 19.6 + - - +
4A PRO* 3.9 9.6 - - + +
6A HIS* 1.3 78.7 - - + +
8A THR* 1.3 61.1 + - - +
10A VAL* 3.5 2.9 + - - +
11A VAL* 3.2 27.3 + - - +
73A ALA* 3.9 12.1 - - + -
74A VAL* 3.8 16.8 - - - +
75A ALA 4.5 0.7 - - - +
76A ASN* 3.7 17.5 - - - +
77A GLU 3.5 36.1 - - - +
78A ALA* 4.4 3.4 - - + -
103A PHE* 3.5 44.1 - - + -
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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 PRO* 2.7 26.4 + - - +
5A GLU* 3.9 6.3 - - - -
7A MET* 1.3 73.2 - - - +
9A ALA* 1.3 64.8 + - - +
11A VAL* 3.3 3.3 + - - +
12A GLN* 3.1 43.1 + - - +
71A VAL* 4.1 32.5 + - + +
73A ALA* 3.9 11.8 - - - +
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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
----------------------------------------------------------
5A GLU* 3.0 16.5 + - + +
6A HIS* 3.1 12.3 + - - +
8A THR* 1.3 76.6 - - - +
10A VAL* 1.3 55.7 + - - +
12A GLN* 3.2 18.1 + - - +
13A ARG* 2.9 55.6 + - + +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 2.9 41.9 + - + +
7A MET 3.7 7.9 - - - +
9A ALA* 1.3 73.7 - - - +
11A VAL* 1.3 60.4 + - - +
13A ARG* 3.4 20.9 + - - +
14A TYR* 3.0 26.2 + - - +
29A LEU* 4.0 22.7 - - + +
101A PHE* 4.3 6.3 - - + -
103A PHE* 3.7 25.6 - - + -
107A GLY 4.5 2.7 - - - +
109A VAL* 4.1 12.6 - - + -
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Residues in contact with VAL 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 MET 3.2 15.4 + - - +
8A THR 3.7 7.6 - - - +
9A ALA 3.3 0.4 - - - -
10A VAL* 1.3 75.4 - - - +
12A GLN* 1.3 58.7 + - - +
14A TYR* 3.5 6.3 + - - +
15A VAL* 3.1 26.9 + - - +
67A LEU* 3.9 9.6 - - + -
71A VAL* 3.8 29.2 - - + -
78A ALA* 4.2 10.1 - - + -
80A PHE* 3.7 50.7 - - + -
101A PHE* 4.2 11.2 - - + -
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.1 32.8 + - + +
9A ALA* 3.2 17.9 + - - +
11A VAL* 1.3 78.1 - - + +
13A ARG* 1.3 60.9 + - + +
15A VAL* 4.0 5.4 - - - +
16A ALA* 3.1 28.6 + - - +
67A LEU* 4.4 18.8 - - + +
71A VAL* 5.5 0.7 - - + -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 4.6 11.9 + - - -
9A ALA* 2.9 40.6 + - - +
10A VAL* 3.8 23.2 - - - +
12A GLN* 1.3 76.1 - - + +
14A TYR* 1.3 58.8 + - - +
16A ALA* 3.9 4.9 - - - +
17A ALA* 3.0 29.6 + - - +
25A GLY 5.2 0.6 - - - +
29A LEU* 4.2 23.0 - - + +
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Residues in contact with TYR 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 VAL 3.0 17.8 + - - +
11A VAL* 3.6 6.1 - - - +
13A ARG* 1.3 74.0 - - - +
15A VAL* 1.3 72.1 + - + +
17A ALA* 3.3 4.8 + - - +
18A LEU* 3.1 46.1 + - + +
26A ILE* 4.1 14.8 - - + +
29A LEU* 3.6 20.1 - - + +
30A PHE* 4.6 7.9 - + - -
38A ASP* 5.3 0.3 + - - -
55A TYR* 3.0 41.5 + + - -
80A PHE* 4.1 13.7 - + - -
82A PHE* 5.4 4.0 - + - -
99A ASP* 3.8 17.0 + - - -
101A PHE* 3.9 28.0 - + + -
112A MET* 3.4 13.6 - - + +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL 3.1 18.0 + - - +
12A GLN* 4.0 6.3 - - - +
14A TYR* 1.3 90.9 - - + +
16A ALA* 1.3 62.8 + - - +
18A LEU* 3.4 5.5 + - - +
19A ASN* 3.2 24.3 + - - +
65A VAL* 3.4 39.5 - - + +
66A GLU* 4.4 6.1 - - - -
67A LEU* 3.9 31.0 - - + +
80A PHE* 4.5 8.5 - - + -
82A PHE* 5.2 2.5 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN 3.1 18.8 + - - +
13A ARG* 3.9 5.8 - - - +
14A TYR 3.2 0.2 - - - -
15A VAL* 1.3 75.3 - - - +
17A ALA* 1.3 60.2 + - - +
19A ASN* 3.3 11.8 + - - +
20A ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 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 ARG 3.0 18.6 + - - +
14A TYR* 3.3 3.1 + - - +
16A ALA* 1.3 73.6 - - - +
18A LEU* 1.3 59.7 + - - +
20A ALA* 3.3 1.4 + - - -
21A GLY* 2.8 24.4 + - - -
22A ASP* 2.9 30.4 + - + +
25A GLY* 4.2 5.8 - - - -
26A ILE* 3.4 34.1 - - + +
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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 TYR* 3.1 41.3 + - + +
15A VAL 3.5 8.1 - - - +
16A ALA 3.2 0.2 - - - -
17A ALA* 1.3 75.8 - - - +
19A ASN* 1.3 63.4 + - - +
21A GLY 3.2 9.4 + - - +
26A ILE* 3.3 27.1 - - + -
55A TYR* 4.1 19.3 - - + -
58A SER* 6.1 0.9 - - - -
59A LEU* 3.6 25.2 - - + +
63A LEU* 4.4 18.6 + - + +
65A VAL* 3.7 28.9 - - + -
82A PHE* 5.3 6.7 - - + -
84A VAL* 5.7 2.9 - - + -
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Residues in contact with ASN 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 VAL* 3.2 21.2 + - - +
16A ALA* 3.5 11.3 - - - +
17A ALA 3.3 0.2 - - - -
18A LEU* 1.3 79.0 - - - +
20A ALA* 1.3 60.6 + - + +
21A GLY 3.8 0.2 + - - -
63A LEU 3.5 11.5 - - - +
64A ALA* 3.4 9.5 - - - -
65A VAL* 2.8 46.6 + - - +
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Residues in contact with ALA 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 ALA 3.0 15.8 + - - +
17A ALA* 3.3 4.2 + - - +
18A LEU 3.2 0.2 - - - -
19A ASN* 1.3 80.4 - - + +
21A GLY* 1.3 61.7 + - - +
22A ASP* 3.5 12.7 + - + +
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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