Contacts of the helix formed by residues 12 - 20 (chain L) in PDB entry 5A31
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 ASP 12 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L GLY 3.8 1.5 + - - -
11L ALA* 1.3 73.8 - - - +
13L PRO* 1.3 77.6 - - - +
14L LYS* 4.1 25.5 - - + +
15L GLN* 2.8 41.5 + - + +
16L LEU* 3.6 3.8 + - - +
18L ARG* 5.3 0.6 + - - +
119L TRP* 3.7 20.5 + - - -
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Residues in contact with PRO 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ALA 3.1 8.2 - - - +
12L ASP* 1.3 85.8 - - - +
14L LYS* 1.3 57.5 + - + +
16L LEU* 3.2 7.6 + - + +
17L GLU* 2.9 33.5 + - - +
78L CYS* 3.5 10.1 - - - -
119L TRP* 3.4 58.1 - - + -
121L HIS* 4.1 12.3 - - + -
157L LYS* 4.2 6.7 - - + +
159L TYR* 3.0 25.3 + - + +
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Residues in contact with LYS 14 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12L ASP* 2.9 19.2 + - - +
13L PRO* 1.3 78.7 - - + +
15L GLN* 1.3 55.1 + - - +
17L GLU* 3.2 22.6 + - - +
18L ARG* 2.8 67.9 + - - +
48L ASP* 5.5 5.8 + - - +
119L TRP* 6.3 1.8 - - - -
157L LYS* 4.0 21.3 - - - +
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Residues in contact with GLN 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ALA* 5.3 6.7 - - + -
12L ASP* 2.8 38.1 + - + +
14L LYS* 1.3 71.6 - - - +
16L LEU* 1.3 60.0 + - - +
18L ARG* 3.2 42.0 + - - +
19L THR* 3.3 17.9 + - - +
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Residues in contact with LEU 16 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12L ASP 3.6 3.6 + - - +
13L PRO* 3.2 11.4 + - + +
15L GLN* 1.3 78.5 - - - +
17L GLU* 1.3 59.5 + - + +
19L THR* 2.4 32.6 + - - +
20L GLY 3.9 0.9 + - - -
21L THR* 4.1 11.2 + - - +
22L VAL* 3.9 23.4 - - + +
76L THR* 4.5 9.4 - - + +
121L HIS* 3.6 31.4 - - + +
159L TYR* 4.4 22.2 - - + -
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L PRO* 2.9 19.0 + - - +
14L LYS* 3.2 27.6 + - - +
16L LEU* 1.3 74.7 - - - +
18L ARG* 1.3 59.9 + - - +
20L GLY* 2.9 22.5 + - - -
22L VAL 4.2 14.2 - - - +
23L ARG* 5.9 0.2 - - - -
24L GLU* 3.0 26.9 - - + +
157L LYS* 4.1 4.5 + - - +
159L TYR* 2.3 47.6 + - + -
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Residues in contact with ARG 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580H GLN 5.2 5.4 - - - +
581H ARG* 5.8 1.4 - - - +
582H GLU* 6.1 0.7 - - - +
12L ASP* 5.3 1.2 + - - +
14L LYS* 2.8 60.2 + - - +
15L GLN* 3.2 43.8 + - - +
17L GLU* 1.3 66.8 - - + +
19L THR* 1.3 66.4 + - - +
20L GLY* 2.9 4.9 + - - -
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Residues in contact with THR 19 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581H ARG* 4.0 13.0 + - - -
15L GLN 3.3 14.1 + - - +
16L LEU* 2.4 31.5 + - - +
18L ARG* 1.3 76.2 - - - +
20L GLY* 1.3 59.7 + - - +
21L THR* 3.2 25.9 + - - +
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Residues in contact with GLY 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581H ARG* 3.6 32.3 + - - -
17L GLU 2.9 17.8 + - - -
18L ARG 2.9 3.6 - - - -
19L THR* 1.3 79.9 + - - +
21L THR* 1.3 62.0 + - - +
22L VAL* 3.3 6.0 + - - +
162L VAL* 3.6 17.2 - - - +
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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