Contacts of the strand formed by residues 52 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.9 0.4 - - + -
50A ALA* 3.5 7.3 - - - +
51A ASP* 1.3 91.3 - - + +
53A ILE* 1.3 60.1 + - - +
54A VAL* 4.2 2.2 - - + -
67A VAL* 2.9 61.2 + - + -
69A LYS* 3.6 38.8 - - + -
100A VAL* 4.7 5.8 - - + -
103A LEU* 3.8 55.0 - - + -
104A LEU* 4.0 22.4 - - + -
61C THR* 3.6 5.4 - - - -
62C ILE* 3.3 28.9 - - + -
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Residues in contact with ILE 53 (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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47A ILE 5.4 0.9 - - - +
50A ALA* 4.5 1.1 - - + -
52A PHE* 1.3 74.9 - - - +
54A VAL* 1.3 69.9 + - - +
55A PRO* 4.2 5.9 - - + +
64A GLN* 3.4 31.4 - - + +
65A VAL 3.4 5.4 - - - +
66A TYR* 3.3 42.0 - - + +
103A LEU* 4.6 1.7 - - - +
61C THR* 3.5 20.2 - - + +
62C ILE 3.1 13.8 + - - +
63C HIS* 3.7 41.5 + - + +
64C GLN 4.8 1.6 + - - -
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Residues in contact with VAL 54 (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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52A PHE* 4.3 7.2 - - + -
53A ILE* 1.3 82.7 - - - +
55A PRO* 1.4 71.9 - - + +
56A VAL* 3.5 15.4 + - + -
65A VAL* 2.8 43.9 + - + +
67A VAL* 4.5 2.7 - - + -
96A TYR* 4.5 4.5 - - + +
99A PRO* 3.7 33.2 - - + +
100A VAL* 4.2 22.2 - - + +
103A LEU* 3.7 25.8 - - + -
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Residues in contact with PRO 55 (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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53A ILE* 4.2 6.1 - - + +
54A VAL* 1.4 88.4 - - + +
56A VAL* 1.3 63.0 + - - +
57A GLU 4.1 1.1 + - - -
62A ILE* 3.8 10.3 - - + -
63A HIS 3.4 5.8 - - - +
64A GLN* 3.8 12.5 - - - +
95A LYS 5.3 1.2 - - - +
99A PRO* 5.7 0.7 - - - +
44C PHE* 3.5 27.1 - - + +
45C LYS* 4.9 1.1 - - - -
46C PRO* 4.5 20.6 - - + +
64C GLN* 6.4 2.0 - - + -
66C TYR* 5.9 2.5 - - + +
900C KEG 2.8 28.9 - - - +
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Residues in contact with VAL 56 (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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54A VAL* 4.1 13.2 - - + -
55A PRO* 1.3 77.6 - - - +
57A GLU* 1.3 70.0 - - - +
58A ILE* 3.7 16.7 + - + +
61A THR 3.6 1.2 - - - +
62A ILE* 4.3 1.8 - - - -
63A HIS* 2.6 47.1 + - + +
65A VAL* 4.1 18.4 - - + -
93A LEU* 4.7 0.9 - - + -
95A LYS* 3.9 28.9 - - + +
96A TYR* 3.8 30.7 - - + +
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Residues in contact with GLU 57 (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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55A PRO 4.1 1.6 + - - -
56A VAL* 1.3 71.4 - - - +
58A ILE* 1.3 62.2 + - - +
60A GLY* 3.8 33.4 + - - +
61A THR 3.4 4.7 - - - -
62A ILE* 3.6 27.5 - - + +
95A LYS* 3.0 44.0 + - - +
45C LYS* 3.8 20.8 + - - -
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Residues in contact with ILE 58 (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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56A VAL* 4.2 12.1 - - + -
57A GLU* 1.3 81.7 - - - +
59A ASP* 1.3 89.1 + - + +
60A GLY 3.2 1.3 - - - -
61A THR* 3.0 26.9 + - - +
63A HIS* 4.0 24.4 - - + +
93A LEU* 3.6 29.6 - - + -
155B GLU* 3.8 19.5 - - + -
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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