Contacts of the helix formed by residues 7 - 22 (chain A) in PDB entry 1H9T
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLN* 1.3 80.4 - - - +
8A PRO* 1.3 78.3 - - - -
9A ALA* 4.5 0.3 - - - +
10A GLY* 2.7 19.8 + - - -
11A PHE* 2.7 11.2 + - - -
7X G 5.2 0.9 - - - -
8X T 3.0 18.6 + - - -
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Residues in contact with PRO 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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6A GLN 4.8 0.2 - - - +
7A SER* 1.3 86.1 - - - +
9A ALA* 1.3 54.2 + - - +
11A PHE* 2.9 8.1 + - + +
12A ALA* 2.6 38.6 + - - +
43A VAL* 4.2 13.9 - - + +
47A THR* 4.3 10.8 - - + -
8X T 4.0 33.0 - - - +
9X A 4.3 9.2 - - - +
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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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7A SER* 2.9 2.2 + - - +
8A PRO* 1.3 78.6 - - - +
10A GLY* 1.3 59.6 + - - +
12A ALA* 3.2 0.9 + - - -
13A GLU* 2.8 31.5 + - - +
47A THR* 4.1 8.8 - - + +
50A GLU* 5.3 5.2 - - + +
51A VAL* 3.7 18.6 - - + +
54A ARG* 4.2 19.1 - - - +
8X T 3.3 27.4 + - - +
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Residues in contact with GLY 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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5A ALA 4.0 4.3 - - - -
6A GLN* 4.4 13.5 - - - -
7A SER* 2.7 17.6 + - - -
9A ALA* 1.3 76.9 - - - +
11A PHE* 1.3 55.6 + - - -
13A GLU* 3.6 9.6 - - - +
14A GLU* 2.7 34.9 + - - +
54A ARG* 5.2 3.3 - - - +
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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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5A ALA* 3.3 31.2 + - + +
6A GLN 5.1 0.2 - - - -
7A SER 2.7 16.5 + - - +
8A PRO* 3.3 11.4 - - + +
10A GLY* 1.3 72.6 - - - +
12A ALA* 1.3 55.3 + - - +
13A GLU 3.0 0.3 + - - -
14A GLU* 3.5 4.7 - - + -
15A TYR* 2.6 62.1 + + + +
41A ILE* 4.4 20.4 - - + -
43A VAL* 5.5 2.5 - - + -
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Residues in contact with ALA 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 PRO 2.6 20.0 + - - +
9A ALA* 3.8 3.1 - - - +
11A PHE* 1.3 74.1 - - - +
13A GLU* 1.3 61.0 + - - +
15A TYR* 3.3 6.0 - - - +
16A ILE* 2.9 31.5 + - + +
41A ILE* 3.9 17.9 - - + -
43A VAL* 3.7 24.7 - - + -
47A THR 5.3 0.2 - - - +
48A LEU* 5.4 2.9 - - + -
51A VAL* 4.1 15.3 - - + -
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Residues in contact with GLU 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 ALA 2.8 21.8 + - - +
10A GLY* 3.6 6.4 - - - +
12A ALA* 1.3 70.2 - - - +
14A GLU* 1.3 70.1 + - - +
15A TYR 2.7 5.1 + - - -
16A ILE* 3.1 0.7 + - - +
17A ILE* 2.8 35.9 + - + +
51A VAL* 3.4 22.8 - - + +
54A ARG* 2.9 30.8 + - - +
55A LEU* 3.9 14.9 - - + +
57B ARG* 2.7 34.7 + - - -
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Residues in contact with GLU 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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5A ALA* 3.8 25.4 + - - -
6A GLN* 4.1 16.9 - - - +
10A GLY 2.7 21.3 + - - +
11A PHE* 3.7 6.8 - - + +
13A GLU* 1.3 75.0 - - - +
15A TYR* 1.3 65.4 + - - +
17A ILE* 3.8 7.2 - - - +
18A GLU* 3.1 21.8 + - - +
88A ARG* 3.3 34.1 + - - +
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Residues in contact with TYR 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* 2.6 47.9 + + + +
12A ALA* 3.3 6.5 - - - +
13A GLU 2.7 2.6 + - - -
14A GLU* 1.3 67.5 - - - +
16A ILE* 1.3 75.0 + - - +
17A ILE 2.5 3.3 + - - -
18A GLU* 2.6 18.5 + - - +
19A SER* 2.9 31.7 + - - -
24A ARG* 2.7 32.8 + - - -
25A PHE* 4.5 10.1 - + - -
37A LEU* 5.5 0.2 - - + -
40A LEU* 3.7 22.0 - - + +
41A ILE* 3.6 39.9 - - + -
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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 ALA 2.9 19.2 + - - +
13A GLU 3.7 1.8 - - - +
15A TYR* 1.3 84.4 - - + +
17A ILE* 1.3 65.9 + - - +
19A SER* 3.3 6.9 + - - -
20A ILE* 3.2 29.7 + - + +
25A PHE* 5.3 6.3 - - + -
31A LEU* 4.9 13.2 - - + -
37A LEU* 4.6 9.2 - - + -
41A ILE* 3.7 17.7 - - + -
48A LEU* 3.8 18.8 - - + -
51A VAL* 4.5 9.0 - - + -
52A LEU* 3.8 26.2 - - + -
55A LEU* 4.2 15.7 - - + -
61A LEU* 5.0 4.0 - - + -
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Residues in contact with ILE 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 GLU* 2.8 41.3 + - + +
14A GLU* 3.8 6.1 - - - +
15A TYR 2.5 4.0 + - - -
16A ILE* 1.3 70.3 - - - +
18A GLU* 1.3 71.1 + - - +
20A ILE* 2.6 21.5 + - - +
21A TRP 3.2 8.3 + - - -
55A LEU* 4.0 25.6 - - + -
60A TRP* 4.2 28.0 - - + +
85A THR* 4.8 9.4 - - - +
88A ARG* 4.5 19.7 - - - +
89A LEU* 4.3 19.7 - - + -
57B ARG* 5.5 3.1 - - - +
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Residues in contact with GLU 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 GLU 3.1 11.2 + - - +
15A TYR* 2.6 13.2 + - - +
17A ILE* 1.3 78.7 - - - +
19A SER* 1.3 65.0 + - - +
20A ILE 2.8 2.3 + - - -
21A TRP* 3.0 7.3 + - + +
22A ASN* 2.7 51.1 + - - +
88A ARG* 5.7 4.7 - - - +
89A LEU* 5.1 11.2 - - + -
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Residues in contact with SER 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 TYR* 2.9 35.5 + - - -
16A ILE 3.4 7.2 - - - -
18A GLU* 1.3 76.4 - - - +
20A ILE* 1.3 62.1 + - - +
22A ASN* 4.0 1.8 - - - -
24A ARG* 3.1 28.3 + - - +
25A PHE* 3.0 53.4 + - - -
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Residues in contact with ILE 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* 3.5 20.6 - - + +
17A ILE* 2.6 15.6 + - - +
19A SER* 1.3 70.8 - - - +
21A TRP* 1.3 55.7 + - - +
22A ASN 2.6 17.0 + - - -
23A ASN* 2.9 14.9 + - - -
25A PHE* 3.9 19.6 - - + +
27A PRO* 4.3 3.7 - - + +
31A LEU* 5.5 0.4 - - + -
55A LEU* 6.0 0.4 - - + -
60A TRP* 3.6 49.6 - - + -
61A LEU* 4.1 16.2 - - + -
71A VAL* 4.1 27.6 - - + -
72A ASN 5.0 0.9 - - - +
235A ALA* 3.5 6.8 - - - +
236A ILE* 4.3 14.8 - - + -
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Residues in contact with TRP 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 ILE* 3.2 6.5 + - + +
18A GLU* 3.0 8.7 + - + +
20A ILE* 1.3 78.7 - - - +
22A ASN* 1.3 78.9 + - - +
60A TRP* 4.8 1.9 - - + -
74A PHE* 4.1 14.6 - + - -
86A LEU* 4.4 10.5 - - + -
89A LEU* 3.5 55.9 + - + -
90A ASP* 3.9 34.5 - - + -
234A LEU* 3.3 32.9 - - + +
235A ALA* 2.5 55.2 + - - -
236A ILE* 3.4 25.8 - - + -
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Residues in contact with ASN 22 (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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18A GLU* 2.7 50.1 + - - +
19A SER* 4.7 2.0 - - - +
20A ILE 2.6 4.2 + - - -
21A TRP* 1.3 94.9 + - - +
23A ASN* 1.3 58.4 + - - +
24A ARG* 2.5 25.6 + - + +
234A LEU* 4.3 14.2 - - - +
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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