Contacts of the helix formed by residues 7 - 22 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B GLN* 1.3 85.9 + - - +
8B PRO* 1.3 75.5 - - - +
10B GLY* 3.0 12.1 + - - -
11B PHE* 2.7 22.1 + - - +
7Y G 4.7 3.6 - - - -
8Y T 2.6 24.7 + - - -
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Residues in contact with PRO 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN 4.1 2.2 - - - +
7B SER* 1.3 87.2 - - - +
9B ALA* 1.3 53.8 + - - +
11B PHE* 3.2 5.8 - - + +
12B ALA* 2.3 41.0 + - - +
43B VAL* 4.1 10.9 - - + +
47B THR* 3.8 9.6 - - + -
8Y T 3.2 32.5 - - - +
9Y C 3.7 22.9 - - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 1.3 79.3 - - - +
10B GLY* 1.3 57.8 + - - +
12B ALA* 4.0 2.5 - - - -
13B GLU* 2.8 34.7 + - - +
47B THR* 3.7 8.9 - - + +
50B GLU* 5.3 4.3 - - + +
51B VAL* 3.8 23.8 - - + +
54B ARG* 4.2 16.4 - - - +
8Y T 3.2 27.0 + - - +
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Residues in contact with GLY 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 4.8 9.9 - - - -
7B SER* 3.0 15.1 + - - -
9B ALA* 1.3 77.7 - - - +
11B PHE* 1.3 57.1 + - - +
13B GLU* 3.9 6.0 - - - +
14B GLU* 3.0 32.9 + - - +
54B ARG* 5.3 4.0 - - - +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA* 3.3 31.8 + - - +
6B GLN 5.0 0.4 - - - +
7B SER 2.7 12.1 + - - +
8B PRO* 2.7 8.2 + - + +
10B GLY* 1.3 73.8 - - - +
12B ALA* 1.3 68.8 + - + +
13B GLU 2.7 6.3 + - - -
14B GLU* 2.9 13.8 + - + +
15B TYR* 2.8 46.5 + + + +
41B ILE* 3.9 28.0 - - + -
43B VAL* 5.1 4.0 - - + -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO 2.3 32.8 + - - +
9B ALA* 3.8 7.2 - - - +
11B PHE* 1.3 68.3 - - - +
13B GLU* 1.3 57.9 + - - +
15B TYR* 4.1 0.4 - - - -
16B ILE* 3.4 27.5 + - - +
41B ILE* 3.6 22.1 - - + +
43B VAL* 3.4 33.0 - - + -
48B LEU* 5.3 3.1 - - + -
51B VAL* 4.2 10.5 - - + -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.6 20.7 + - - -
9B ALA 2.8 16.7 + - - +
10B GLY* 3.9 3.8 - - - +
11B PHE 2.7 3.4 + - - -
12B ALA* 1.3 70.8 - - - +
14B GLU* 1.3 66.8 + - - +
15B TYR 2.5 6.5 + - - -
16B ILE* 2.7 15.8 + - - +
17B ILE* 3.0 35.7 + - + +
51B VAL* 3.1 22.6 - - + +
54B ARG* 2.9 39.4 + - - -
55B LEU* 3.8 13.6 - - + +
58B ASP* 5.1 1.2 - - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA 3.9 25.6 + - - +
6B GLN* 4.5 9.2 - - - +
10B GLY 3.0 19.8 + - - +
11B PHE* 3.3 12.2 - - + +
13B GLU* 1.3 77.9 - - - +
15B TYR* 1.3 65.4 + - - +
17B ILE* 3.7 8.8 + - - +
18B GLU* 3.1 21.8 + - + +
88B ARG* 2.9 35.1 + - - +
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Residues in contact with TYR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 2.8 35.8 + + + +
12B ALA* 3.6 6.7 - - - +
13B GLU 2.5 5.8 + - - -
14B GLU* 1.3 69.9 - - - +
16B ILE* 1.3 60.1 + - - +
17B ILE 2.5 15.8 + - - -
18B GLU* 2.7 18.9 + - - +
19B SER* 3.0 30.4 + - - -
24B ARG* 5.8 3.9 - - - -
25B PHE* 3.7 18.8 - + - -
37B LEU* 5.4 0.2 - - + -
40B LEU* 3.8 28.2 - - + +
41B ILE* 3.4 44.2 - - + -
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 3.4 14.3 + - - +
13B GLU 2.7 9.5 + - - +
15B TYR* 1.3 81.4 - - + +
17B ILE* 1.3 59.3 + - - +
19B SER* 4.0 4.8 + - - -
20B ILE* 3.1 31.6 + - + +
25B PHE* 4.5 5.0 - - + -
31B LEU* 4.7 8.7 - - + -
37B LEU* 4.1 15.7 - - + -
41B ILE* 3.8 12.6 - - + -
48B LEU* 3.8 29.2 - - + -
51B VAL* 4.8 1.6 - - + -
52B LEU* 3.8 15.3 - - + -
55B LEU* 3.8 25.1 - - + -
61B LEU* 4.7 11.7 - - + -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.3 44.2 - - + +
14B GLU* 3.8 8.5 - - - +
15B TYR 2.5 5.3 + - - -
16B ILE* 1.3 72.5 - - - +
18B GLU* 1.3 58.4 + - - +
20B ILE* 2.7 32.6 + - - +
21B TRP* 3.0 9.9 + - - +
55B LEU* 3.7 23.8 - - + -
60B TRP* 4.3 27.5 - - + +
85B THR* 4.2 23.8 - - + +
88B ARG* 4.9 9.0 - - - +
89B LEU* 4.5 11.0 - - + -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU 3.1 15.5 + - - +
15B TYR* 2.7 9.9 + - - +
17B ILE* 1.3 76.2 - - - +
19B SER* 1.3 76.4 + - - +
21B TRP* 2.8 24.9 + - - +
22B ASN* 2.7 39.8 + - - +
24B ARG* 3.6 25.8 + - - -
88B ARG* 6.0 1.8 - - - +
89B LEU* 4.7 18.1 - - + +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.0 37.1 + - - -
16B ILE 4.2 1.1 - - - -
18B GLU* 1.3 86.0 + - - +
20B ILE* 1.3 58.9 + - - +
22B ASN 4.0 1.3 - - - +
23B ASN 3.8 0.2 + - - -
24B ARG* 3.0 45.8 + - - +
25B PHE* 2.9 38.9 + - - -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.1 23.6 - - + +
17B ILE* 2.7 14.0 + - - +
19B SER* 1.3 71.7 - - - +
21B TRP* 1.3 66.5 + - - +
22B ASN 3.0 5.2 + - - -
23B ASN* 3.4 11.8 + - - -
25B PHE* 4.0 21.7 - - + +
27B PRO* 5.1 10.5 - - + +
31B LEU* 5.8 0.7 - - + -
60B TRP* 4.2 43.7 - - + -
61B LEU* 4.3 12.8 - - + -
71B VAL* 4.0 29.8 - - + -
72B ASN 5.2 0.2 - - - +
74B PHE* 4.5 13.2 - - + -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.0 7.8 + - + +
18B GLU* 2.8 7.9 + - - +
20B ILE* 1.3 81.2 - - - +
22B ASN* 1.3 94.4 + - - +
23B ASN* 3.6 4.4 + - - -
60B TRP* 5.3 7.1 - + + -
74B PHE* 3.6 38.8 - + - -
75B TRP* 4.7 12.1 - + - -
86B LEU* 3.9 24.5 - - + -
89B LEU* 3.4 53.1 + - + +
90B ASP* 3.8 30.7 - - + +
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 2.7 45.8 + - - +
19B SER 4.0 1.1 - - - -
20B ILE 3.0 0.2 + - - -
21B TRP* 1.3 120.1 + - - +
23B ASN* 1.3 56.8 + - - +
24B ARG* 2.8 31.8 + - - +
89B LEU* 5.5 0.7 - - - +
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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