Contacts of the strand formed by residues 40 - 44 (chain A) in PDB entry 2HDH
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 2.8 13.1 + - - +
17A HIS* 3.4 28.6 + - + +
18A VAL 2.8 26.5 + - - -
38A GLY 4.0 1.6 + - - -
39A HIS* 1.3 71.2 - - - +
41A VAL* 1.3 64.7 + - - +
87A THR* 4.1 15.6 - - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A HIS* 4.8 0.2 - - - -
18A VAL* 3.4 11.2 - - + +
20A VAL* 4.3 6.7 - - + -
31A ALA* 3.9 27.6 - - + +
34A ALA* 3.8 15.7 - - + -
35A ALA* 3.7 24.0 - - + +
39A HIS* 3.7 13.2 - - + +
40A THR* 1.3 82.6 - - - +
42A VAL* 1.3 72.7 + - - +
43A LEU 4.2 2.2 - - - +
87A THR 2.9 14.5 + - - +
88A ILE* 3.3 10.2 - - + -
89A ALA* 2.8 32.1 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A HIS* 3.3 35.2 - - + +
18A VAL 3.0 6.4 + - - +
19A THR* 3.6 4.1 - - + +
20A VAL 2.9 27.2 + - - +
40A THR* 5.7 0.2 - - + -
41A VAL* 1.3 78.4 - - - +
43A LEU* 1.3 62.1 + - - +
44A VAL* 3.7 11.2 + - + -
89A ALA* 3.4 20.0 - - + +
91A SER* 3.8 24.0 - - - +
97A VAL* 3.8 30.3 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.5 25.1 - - + +
22A GLY 3.7 20.0 - - - +
23A GLY* 4.1 5.8 - - - -
27A GLY 4.2 3.6 - - - +
28A ALA* 5.0 0.4 - - - -
31A ALA* 4.0 13.7 - - + -
41A VAL* 4.1 1.8 - - - +
42A VAL* 1.3 71.7 - - - +
44A VAL* 1.3 59.4 + - - +
51A LEU* 3.5 16.8 - - + +
54A SER* 3.9 27.8 - - - -
55A LYS* 4.6 4.9 - - - +
58A ILE* 4.2 19.5 - - + -
88A ILE* 4.3 9.6 - - + -
89A ALA 2.8 13.0 + - - +
90A THR* 3.3 13.8 - - + -
91A SER 3.1 22.5 + - - -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.9 28.0 - - + -
20A VAL 2.8 12.7 + - - +
21A ILE* 4.1 15.3 - - + +
22A GLY* 2.7 32.6 + - - -
42A VAL* 4.1 11.2 - - + -
43A LEU* 1.3 79.2 - - - +
45A ASP* 1.3 67.5 + - - +
51A LEU* 3.8 1.3 - - - -
91A SER* 3.2 16.8 - - - +
92A THR 4.1 8.1 - - - +
94A ALA* 3.7 37.2 - - + +
350A NAD 5.1 3.8 - - + -
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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