Contacts of the strand formed by residues 12 - 19 (chain D) in PDB entry 5HVO
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 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D HIS* 1.3 78.9 - - + +
13D LEU* 1.3 60.6 + - - +
14D LEU* 3.8 13.1 - - + +
53D THR* 3.7 26.5 + - + +
54D PHE 5.2 0.4 + - - -
55D GLN* 3.8 35.6 + - - +
57D TYR* 4.5 4.9 + - - -
81D ASN* 5.9 0.4 - - - +
139D GLU* 4.6 11.7 + - - +
141D GLN* 5.1 8.3 - - - +
143D GLY 4.7 3.6 + - - +
144D ASP* 3.0 41.5 + - - +
145D LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D HIS 3.9 0.6 + - - -
12D ARG* 1.3 74.3 - - - +
14D LEU* 1.3 72.6 + - - +
15D ILE* 3.8 20.8 + - + +
49D SER* 5.8 0.7 - - - +
52D THR* 5.0 8.3 - - - +
53D THR 2.8 14.8 + - - +
54D PHE* 3.2 25.5 - - + +
55D GLN 3.1 22.7 + - - -
145D LEU* 3.5 34.3 - - + +
146D ILE 4.5 0.2 - - - -
147D TRP* 3.8 24.0 - - + -
471D VAL* 3.9 26.7 - - + -
474D LEU* 5.1 1.8 - - + -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.8 39.5 - - + +
13D LEU* 1.3 80.1 - - - +
15D ILE* 1.3 61.7 + - - +
16D VAL* 4.0 1.7 + - + -
55D GLN* 3.4 9.2 - - + -
57D TYR* 3.5 30.3 - - + +
136D ILE* 4.5 7.6 - - + -
139D GLU 5.1 0.7 - - - +
140D ALA* 4.3 19.3 - - + -
144D ASP* 3.7 25.6 - - + +
145D LEU 2.7 11.6 + - - +
146D ILE* 3.5 21.7 - - + +
147D TRP 2.8 27.5 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.9 19.3 - - + -
14D LEU* 1.3 75.5 - - - +
16D VAL* 1.3 64.9 + - - +
17D SER* 5.7 1.6 - - - +
45D LEU* 4.3 15.9 - - + -
54D PHE* 4.0 31.4 - - + -
55D GLN 3.0 7.9 + - - +
56D TRP* 3.6 51.5 - - + -
57D TYR 2.9 26.9 + - - +
147D TRP* 3.7 16.4 - - + +
149D GLN* 4.5 11.4 - - + +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU 4.3 2.9 - - - +
15D ILE* 1.3 79.8 - - - +
17D SER* 1.3 63.2 + - - +
57D TYR* 3.5 12.8 - - + +
132D PHE* 3.5 32.5 - - + -
136D ILE* 3.6 24.0 - - + -
146D ILE* 4.0 22.7 - - + -
147D TRP 2.9 9.8 + - - +
148D VAL* 4.3 9.6 - - + -
149D GLN* 2.9 34.5 + - - +
153D LEU* 3.9 2.9 - - + -
156D LEU* 3.8 15.3 - - + -
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 5.7 1.7 - - - +
16D VAL* 1.3 76.6 - - - +
18D ASN* 1.3 66.1 + - - +
19D ARG 2.9 22.8 + - - -
21D PRO* 5.1 4.9 - - - +
45D LEU* 6.4 1.3 - - - -
56D TRP* 5.4 6.1 - - - -
57D TYR 3.1 6.1 + - - -
58D GLY* 3.2 19.1 - - - -
132D PHE* 3.3 6.8 - - - -
149D GLN* 4.1 18.2 - - - -
150D ASP* 6.3 0.2 - - - -
153D LEU* 3.9 12.6 - - - -
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Residues in contact with ASN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 1.3 74.3 - - - +
19D ARG* 1.3 71.0 + - + +
59D TRP* 2.9 40.9 + - - +
87D MET* 4.9 2.8 - - - +
95D HIS* 3.4 32.5 + - - -
96D TYR* 3.5 24.6 - - - -
132D PHE* 3.8 11.8 - - - -
149D GLN 4.8 1.8 + - - -
152D HIS* 3.7 35.7 + - + +
153D LEU* 4.0 6.0 - - - +
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Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 2.9 22.1 + - - +
18D ASN* 1.3 88.8 + - + +
20D LEU* 1.3 69.2 + - - +
21D PRO* 3.7 0.7 - - - +
58D GLY* 4.1 4.6 - - - -
59D TRP* 3.1 38.5 - - + +
60D PRO 5.8 0.2 - - - -
61D GLY* 4.4 12.3 + - - +
96D TYR* 3.1 47.7 + - - -
502D VDM 6.1 0.4 - - - -
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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