Contacts of the strand formed by residues 50 - 54 (chain E) in PDB entry 4HHM
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 GLY 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E PHE 3.3 4.3 + - - +
12E THR* 3.3 16.9 - - - +
13E PHE* 3.3 18.2 + - - +
48E ALA* 3.7 3.0 - - - +
49E TYR* 1.3 82.4 - - - +
51E VAL* 1.3 68.5 + - - +
84E MET* 3.7 10.5 - - - +
85E THR* 3.2 17.0 - - - -
87E PRO* 4.5 0.2 - - - -
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E PHE 3.1 8.7 - - - +
15E LEU* 4.4 17.7 - - + -
40E VAL* 4.3 9.9 - - + -
43E LEU* 3.4 30.3 - - + -
50E GLY* 1.3 78.5 - - - +
52E THR* 1.3 64.1 + - - +
75E PHE* 3.9 20.0 - - + -
79E LEU* 3.9 27.6 - - + -
84E MET* 3.7 9.9 - - + -
85E THR 2.9 4.5 + - - +
86E VAL* 3.3 29.0 - - + +
87E PRO* 3.7 3.8 - - - +
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Residues in contact with THR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 4.8 6.5 - - - +
13E PHE 2.9 4.2 + - - -
14E GLY* 3.0 11.4 - - - -
15E LEU* 2.9 29.0 + - - +
16E TRP* 3.4 4.4 - - - -
51E VAL* 1.3 77.7 - - - +
53E PHE* 1.3 65.8 + - - +
87E PRO* 4.9 1.8 - - + -
88E MET* 3.4 49.6 - - + +
243E HIS* 4.5 1.3 - - - +
285E HIS* 2.8 40.3 + - + -
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Residues in contact with PHE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 3.5 22.7 - - + -
16E TRP* 4.1 5.1 - - - -
52E THR* 1.3 78.2 - - - +
54E HIS* 1.3 79.9 + - - +
55E ASP* 4.4 1.6 - - - -
57E ASP* 4.2 3.4 - - + -
58E LEU* 3.6 26.0 - - + -
75E PHE* 5.1 3.6 - + - -
86E VAL* 3.7 20.6 - - + -
88E MET 3.7 1.6 + - - -
89E ALA* 3.4 26.9 - - + +
90E THR* 2.9 31.4 + - - +
122E ASN* 3.6 24.9 - - - -
125E LEU* 4.1 10.1 - - + -
126E ALA* 4.7 3.6 - - - -
129E LEU* 3.5 33.7 - - + -
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Residues in contact with HIS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E TRP* 3.2 46.9 - + - -
53E PHE* 1.3 84.3 - - - +
55E ASP* 1.3 66.9 + - - +
56E ASP 4.1 1.8 - - - +
57E ASP* 2.9 46.4 + - - +
58E LEU 3.5 0.3 + - - -
90E THR* 3.3 26.9 + - + +
91E THR 3.7 17.7 + - - -
92E ASN* 3.9 17.3 - - + +
94E PHE* 3.9 29.5 - + - -
137E TRP* 5.3 4.0 - - - -
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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