Contacts of the strand formed by residues 12 - 16 (chain D) in PDB entry 1H4O
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 VAL 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D PRO* 2.8 31.6 + - + +
11D ALA* 1.3 75.7 - - - +
13D GLU* 1.3 73.5 + - - +
14D VAL* 3.7 11.7 + - + -
24D ASN* 4.1 1.3 + - - -
25D LEU* 3.0 28.2 + - + +
103D ALA* 3.9 24.7 - - + +
104D PHE* 4.0 31.4 - - + +
107D GLU* 4.3 15.5 - - + -
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Residues in contact with GLU 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 ALA 3.7 2.9 + - - +
12D VAL* 1.3 77.9 - - - +
14D VAL* 1.3 75.6 + - - +
15D PHE* 4.0 25.2 - - + -
22D LYS* 3.6 39.8 + - + +
23D VAL 3.5 9.0 - - - +
24D ASN* 4.5 6.3 - - + +
99D ASP* 4.8 3.5 - - - +
103D ALA* 5.3 1.7 - - - +
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Residues in contact with VAL 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 VAL* 4.2 15.5 - - + +
13D GLU* 1.3 81.0 - - - +
15D PHE* 1.3 75.1 + - - +
22D LYS* 3.5 0.9 - - - -
23D VAL* 2.8 43.6 + - + +
25D LEU* 4.1 18.2 - - + -
73D LEU* 4.0 9.0 - - + -
97D LEU* 4.0 30.3 - - + -
98D ALA 3.4 16.6 - - - +
99D ASP* 4.0 20.0 - - + +
104D PHE* 5.4 0.2 - - + -
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Residues in contact with PHE 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 GLU* 4.0 24.2 - - + -
14D VAL* 1.3 89.0 - - - +
16D GLU* 1.3 61.4 + - - +
18D GLU 4.2 0.4 - - - +
19D PRO* 3.0 28.3 - - + +
21D ASN 3.1 13.2 - - - +
22D LYS* 3.8 26.5 - - + -
23D VAL* 4.9 0.7 - - - -
78D ALA* 4.1 16.2 - - + -
97D LEU* 3.3 7.6 - - - -
98D ALA* 2.7 46.1 + - + +
99D ASP* 5.6 0.4 - - - -
100D PRO* 3.9 22.9 - - + -
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Residues in contact with GLU 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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15D PHE* 1.3 77.6 - - - +
17D GLY* 1.3 59.2 + - - +
18D GLU 2.9 11.2 + - - -
21D ASN* 2.9 32.9 + - + +
23D VAL* 3.7 13.7 - - + +
78D ALA* 4.5 0.4 - - - +
95D ARG* 2.8 56.4 + - - +
96D LEU* 3.4 18.1 + - + +
97D LEU* 3.9 12.1 - - + +
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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