Contacts of the strand formed by residues 52 - 58 (chain D) in PDB entry 2HHL
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 PHE 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D VAL* 5.0 0.4 - - + -
50D ALA* 3.9 2.5 - - - +
51D ASP* 1.3 89.6 - - + +
53D ILE* 1.3 70.4 + - - +
54D VAL* 4.2 4.3 - - + -
66D TYR* 3.7 0.2 - - - -
67D VAL* 2.9 57.7 + - + +
69D LYS* 3.6 38.4 - - + -
100D VAL* 4.5 10.1 - - + -
103D LEU* 3.4 64.8 - - + -
104D LEU* 4.2 15.9 - - + -
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Residues in contact with ILE 53 (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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50D ALA* 4.4 8.7 - - + +
52D PHE* 1.3 80.3 - - - +
54D VAL* 1.3 65.3 + - - +
55D PRO* 4.0 6.6 - - + +
64D GLN* 3.5 42.2 - - + +
65D VAL 3.4 8.5 - - - +
66D TYR* 3.8 29.4 - - + +
103D LEU* 5.2 2.9 - - - +
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 4.4 1.8 - - + -
53D ILE* 1.3 78.1 - - - +
55D PRO* 1.3 71.7 - - + +
56D VAL* 3.5 19.8 + - + -
64D GLN* 4.6 1.3 - - - -
65D VAL* 2.8 43.5 + - + +
67D VAL* 4.3 8.5 - - + -
96D TYR* 4.7 5.8 - - + +
99D PRO* 3.7 28.9 - - + -
100D VAL* 4.1 22.9 - - + -
103D LEU* 4.2 21.5 - - + -
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Residues in contact with PRO 55 (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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53D ILE* 4.0 6.3 - - + +
54D VAL* 1.3 88.8 - - + +
56D VAL* 1.3 61.8 + - - +
57D GLU 4.3 0.6 + - - -
62D ILE* 3.7 21.5 - - + -
63D HIS 3.6 7.0 - - - +
64D GLN* 4.6 6.5 - - + +
95D LYS 5.1 1.4 - - - +
99D PRO* 5.8 1.0 - - - +
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Residues in contact with VAL 56 (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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54D VAL* 3.8 17.7 - - + -
55D PRO* 1.3 77.3 - - - +
57D GLU* 1.3 63.9 + - - +
58D ILE* 3.7 11.8 + - + -
61D THR 3.6 1.2 - - - +
62D ILE* 3.5 3.2 - - - +
63D HIS* 2.8 42.4 + - + +
65D VAL* 3.5 30.5 - - + -
95D LYS* 3.6 46.0 - - + +
96D TYR* 4.3 12.1 - - + +
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Residues in contact with GLU 57 (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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55D PRO 4.3 0.6 - - - -
56D VAL* 1.3 72.8 - - - +
58D ILE* 1.3 59.4 + - - +
59D ASP 4.2 0.2 - - - -
60D GLY* 3.5 42.3 + - - +
61D THR 3.4 3.4 - - - +
62D ILE* 3.1 30.2 - - + +
95D LYS* 2.8 32.2 + - + +
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Residues in contact with ILE 58 (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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44D PHE* 3.7 32.3 - - + -
56D VAL* 4.5 15.0 - - + +
57D GLU* 1.3 78.1 - - - +
59D ASP* 1.3 76.8 + - + +
61D THR* 2.8 28.0 + - - +
63D HIS* 4.0 22.0 + - + +
95D LYS* 4.2 10.8 - - + +
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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