Contacts of the strand formed by residues 48 - 52 (chain A) in PDB entry 1H8O
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 LYS 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.4 6.0 - - - -
40A GLN* 2.8 60.8 + - - +
46A SER 4.6 3.1 - - - +
47A PRO* 1.3 75.3 - - - +
49A LEU* 1.3 72.9 + - - +
50A LEU* 3.5 13.4 + - + +
60A GLY* 5.7 2.5 - - - -
61A VAL* 5.1 14.0 - - - +
62A PRO* 5.5 4.4 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 3.9 16.4 - - + -
38A TRP 3.8 7.0 - - - +
39A TYR* 3.3 36.8 - - + +
47A PRO 4.2 0.6 + - - -
48A LYS* 1.3 82.8 - - - +
50A LEU* 1.3 63.6 + - - +
51A ILE 4.0 7.6 - - - +
52A TYR* 4.3 7.6 - - + -
58A HIS* 3.3 44.4 + - + +
61A VAL* 3.9 6.4 - - - +
230A TRP* 4.1 25.4 - - + +
231A GLY* 4.2 25.2 + - - +
233A TRP* 5.6 1.6 - - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 2.9 15.4 + - + +
39A TYR 4.5 1.6 - - - -
40A GLN* 3.9 24.2 - - + +
48A LYS* 4.2 13.2 - - - +
49A LEU* 1.3 77.0 - - - +
51A ILE* 1.3 74.8 + - + +
57A ARG* 3.7 0.9 - - - -
58A HIS* 3.0 25.2 + - - -
61A VAL* 3.3 36.2 - - + +
62A PRO* 5.7 0.4 - - + -
65A PHE* 3.8 24.7 - - + -
76A LEU* 4.5 7.6 - - + -
89A TYR* 3.5 37.7 - - + -
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Residues in contact with ILE 51 (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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37A ALA* 2.9 7.4 - - - +
38A TRP* 2.8 43.6 + - + -
49A LEU* 4.0 3.1 - - - +
50A LEU* 1.3 92.4 - - + +
52A TYR* 1.3 66.5 + - - +
54A ALA* 3.5 31.0 - - - +
55A SER* 3.9 5.4 - - - +
56A THR 3.3 13.9 - - - +
57A ARG* 4.1 10.1 - - + -
65A PHE* 4.4 7.9 - - + +
66A THR* 3.7 13.5 - - - +
67A GLY* 3.4 27.4 - - - +
76A LEU* 3.8 18.6 - - + -
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Residues in contact with TYR 52 (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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36A VAL 3.6 4.9 - - - -
37A ALA* 4.2 2.9 - - + +
49A LEU* 4.3 13.9 - - + -
51A ILE* 1.3 77.0 - - - +
53A TRP* 1.3 91.1 + + - +
54A ALA 3.1 2.2 - - - -
56A THR* 2.8 71.1 + - + +
57A ARG 4.4 1.9 + - - -
58A HIS* 3.9 26.9 - + + -
59A THR* 5.6 0.9 + - - -
94A TYR* 4.2 2.5 - - - +
230A TRP* 3.7 40.8 - + + -
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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