Contacts of the helix formed by residues 11 - 21 (chain B) in PDB entry 3H90
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 ARG 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B SER* 1.3 80.3 + - - +
12B ALA* 1.3 55.9 + - - +
13B ALA* 3.1 8.1 - - - +
14B ILE* 3.4 40.3 - - - +
64B LEU* 4.4 23.8 - - + +
79B GLU* 2.6 33.3 + - - -
142B THR* 2.8 25.1 + - - +
143B GLN* 4.4 2.2 - - - +
144B SER* 3.3 35.0 - - - +
240B GLY 4.8 1.4 - - - -
241B PRO* 3.5 41.4 - - + +
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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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9B VAL* 4.9 11.7 - - + -
10B SER* 3.2 12.0 + - - +
11B ARG* 1.3 74.9 - - - +
13B ALA* 1.3 58.0 + - - +
14B ILE 3.1 1.1 - - - -
15B ALA* 3.3 13.3 + - + +
16B ALA* 2.9 29.9 + - - +
64B LEU* 5.9 0.4 - - - -
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Residues in contact with ALA 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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9B VAL* 5.1 11.3 - - + +
10B SER 3.6 17.2 + - - +
11B ARG 4.7 0.2 - - - -
12B ALA* 1.3 77.9 - - - +
14B ILE* 1.3 58.2 + - - +
16B ALA* 3.4 17.6 - - - +
17B THR* 3.5 4.3 + - - +
134B PHE* 5.0 0.2 - - - -
137B TRP* 5.6 8.7 - - + -
138B VAL* 3.4 23.5 - - + +
141B ARG* 5.6 7.0 - - + -
142B THR* 4.1 18.4 - - + -
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Residues in contact with ILE 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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11B ARG* 3.4 37.9 + - - +
12B ALA 3.1 0.8 - - - -
13B ALA* 1.3 73.4 - - - +
15B ALA* 1.3 67.5 + - - +
16B ALA 3.0 1.8 - - - -
17B THR* 3.1 23.1 - - - +
18B ALA* 3.1 10.2 + - - +
60B VAL* 3.5 37.4 - - + +
63B SER* 5.2 0.4 - - - +
64B LEU* 4.0 12.3 - - + -
79B GLU* 4.7 3.6 - - - +
138B VAL* 4.0 2.0 - - + -
142B THR* 3.6 35.2 - - + +
144B SER* 3.7 20.2 - - - +
147B VAL* 3.8 12.3 - - + +
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Residues in contact with ALA 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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12B ALA* 3.3 18.5 + - + +
14B ILE* 1.3 85.5 - - + +
16B ALA* 1.3 60.8 + - - +
18B ALA* 3.3 14.1 - - - +
19B MET* 3.1 23.2 - - - +
57B LEU* 4.2 1.6 - - + +
60B VAL* 4.5 7.4 - - + -
61B ARG* 5.1 19.5 - - + +
64B LEU* 4.7 12.1 - - + -
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Residues in contact with ALA 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 2.9 12.4 + - - +
13B ALA* 3.4 15.3 - - - +
14B ILE 3.0 0.2 - - - -
15B ALA* 1.3 73.2 - - - +
17B THR* 1.3 58.1 + - - +
18B ALA 2.9 3.8 - - - -
19B MET* 2.8 30.0 + - - +
20B ALA* 2.9 10.2 + - - +
134B PHE* 4.4 15.7 - - + -
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Residues in contact with THR 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 ALA 3.5 12.5 + - - +
14B ILE 3.1 16.8 - - - +
16B ALA* 1.3 75.0 - - - +
18B ALA* 1.3 60.0 + - - +
20B ALA* 3.4 12.3 - - - +
21B SER* 3.3 20.8 + - - -
134B PHE* 3.9 8.2 - - - -
135B GLN* 3.2 29.3 + - - +
138B VAL* 3.5 32.1 - - + -
147B VAL* 3.6 20.7 - - + +
150B ASP* 4.8 1.4 - - - +
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Residues in contact with ALA 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 ILE 3.1 10.6 + - - +
15B ALA 3.3 13.9 - - - +
16B ALA 2.9 0.6 + - - -
17B THR* 1.3 77.9 - - - +
19B MET* 1.3 63.1 + - - +
21B SER* 3.4 9.2 + - - -
22B LEU* 3.3 20.7 - - - +
53B SER 4.4 4.5 - - - +
56B ASN* 5.1 4.5 - - + +
57B LEU* 3.6 37.0 - - + +
60B VAL* 4.2 9.9 - - + -
147B VAL* 6.1 1.6 - - + -
150B ASP* 5.5 3.1 - - - -
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Residues in contact with MET 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 ALA 3.1 27.1 - - - +
16B ALA* 2.8 12.1 + - - +
18B ALA* 1.3 71.6 - - - +
20B ALA* 1.3 58.6 + - - +
21B SER 3.0 2.2 - - - -
22B LEU* 2.6 44.1 + - + +
23B LEU 3.5 0.2 + - - -
57B LEU* 4.3 14.6 - - + -
61B ARG* 3.4 40.8 - - - +
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Residues in contact with ALA 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 ALA 2.9 5.5 + - - +
17B THR* 3.4 23.6 - - - +
18B ALA 3.3 0.2 - - - -
19B MET* 1.3 77.0 - - - +
21B SER* 1.3 55.4 + - - +
23B LEU* 3.1 27.8 - - - +
131B LEU* 3.2 16.5 - - + +
134B PHE* 3.5 27.6 - - + -
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Residues in contact with SER 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 THR 3.3 4.6 + - - -
18B ALA 3.7 8.1 - - - -
19B MET 2.9 1.2 + - - -
20B ALA* 1.3 73.6 - - - +
22B LEU* 1.3 58.8 + - - +
23B LEU 3.0 5.2 - - - -
24B LEU* 3.2 25.2 + - - +
49B ASP 5.2 0.9 - - - +
50B ILE* 5.7 0.2 - - - -
53B SER* 3.5 27.3 - - - -
131B LEU* 3.8 8.5 - - - +
135B GLN* 3.0 29.1 + - - -
150B ASP* 3.1 9.1 + - - -
154B TYR* 3.3 14.1 + - - -
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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