Contacts of the strand formed by residues 75 - 79 (chain E) in PDB entry 3HN3
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 VAL 75 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ASN* 6.1 0.7 - - - +
46E SER* 3.5 3.8 - - - -
47E PHE* 2.8 60.1 + - + +
48E ARG* 5.6 0.2 - - - -
73E PRO* 6.5 0.2 - - + -
74E THR* 1.3 79.3 - - - +
76E ASP* 1.3 71.9 + - - +
77E MET* 4.5 4.5 - - + -
92E LEU* 6.1 1.6 - - + -
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Residues in contact with ASP 76 (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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367B VAL* 3.9 18.5 - - + +
371B ASN* 5.4 1.0 + - - -
395B MET* 3.9 4.0 - - - +
398B ARG* 2.8 42.8 + - - -
399B TYR* 2.6 30.9 + - - +
44E LEU* 4.0 27.5 - - + +
45E TRP 3.5 7.9 - - - +
46E SER* 5.3 3.6 + - - -
75E VAL* 1.3 83.6 - - - +
77E MET* 1.3 65.2 + - - +
78E PRO 4.3 0.2 - - - -
86E ILE* 5.0 0.3 - - - +
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Residues in contact with MET 77 (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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44E LEU* 4.7 2.5 - - - -
45E TRP* 2.8 37.2 + - - +
47E PHE* 3.5 47.8 - - + -
75E VAL* 4.5 4.7 - - + -
76E ASP* 1.3 80.3 - - - +
78E PRO* 1.3 85.0 - - + +
79E VAL* 4.0 0.7 - - - +
81E SER 5.9 0.2 - - - +
82E SER 4.7 0.4 - - - +
83E PHE* 3.6 31.4 - - + +
86E ILE* 3.9 17.0 - - + -
87E SER* 5.8 2.2 - - - -
92E LEU* 4.6 6.5 - - + -
101E TYR* 3.6 30.1 - - + +
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Residues in contact with PRO 78 (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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363B TRP* 3.9 15.5 - - + +
364B PRO* 3.8 30.1 - - + -
367B VAL* 4.0 17.4 - - + -
43E GLY 3.4 8.3 - - - +
44E LEU* 4.7 2.5 - - + -
77E MET* 1.3 104.5 - - - +
79E VAL* 1.3 63.2 + - - +
80E PRO 5.0 0.2 - - - +
81E SER* 3.4 21.8 + - - +
86E ILE* 3.8 28.3 - - + -
101E TYR* 4.8 0.3 - - - -
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Residues in contact with VAL 79 (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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363B TRP* 5.1 4.2 - - - -
42E ASP* 3.2 14.1 - - - +
43E GLY* 2.8 37.4 + - - -
45E TRP* 3.4 41.3 - - + +
77E MET 4.0 0.7 - - - +
78E PRO* 1.3 79.0 - - - +
80E PRO* 1.3 73.5 - - + +
101E TYR* 3.8 21.3 - - + -
214E LEU* 3.6 27.8 - - + +
216E ARG 4.3 7.4 - - - +
218E VAL* 4.4 7.9 - - + -
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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