Contacts of the strand formed by residues 50 - 54 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F PHE 3.3 2.9 + - - +
12F THR* 3.2 29.0 - - - -
13F PHE* 3.4 2.3 + - - -
48F ALA* 3.8 4.1 - - - +
49F TYR* 1.3 82.5 + - - +
51F VAL* 1.3 70.3 + - - +
84F MET* 3.8 7.7 - - - +
85F THR* 3.1 20.4 - - - -
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE 3.2 10.5 - - - +
15F LEU* 4.1 15.7 - - + -
40F VAL* 4.5 10.8 - - + -
43F LEU* 3.9 28.0 - - + -
50F GLY* 1.3 81.9 - - - +
52F THR* 1.3 65.4 + - - +
53F PHE* 6.1 0.2 - - + -
75F PHE* 3.9 28.5 - - + -
79F LEU* 4.4 10.5 - - + -
84F MET* 4.7 10.3 - - + -
85F THR 2.8 12.4 + - - +
86F VAL* 3.2 28.2 - - + +
87F PRO* 3.4 5.4 - - - +
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Residues in contact with THR 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F THR* 4.5 6.1 - - - +
13F PHE 2.9 5.5 + - - -
14F GLY* 3.2 9.9 - - - -
15F LEU* 3.1 24.9 + - - +
16F TRP* 3.2 5.9 - - - -
51F VAL* 1.3 79.8 - - - +
53F PHE* 1.3 68.8 + - - +
87F PRO* 4.9 2.5 - - + -
88F MET* 3.2 46.9 - - + +
243F HIS* 4.6 0.9 - - - +
285F HIS* 2.8 42.9 + - + +
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Residues in contact with PHE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 3.6 23.6 - - + -
16F TRP* 3.6 14.7 - - - -
51F VAL 5.5 0.2 - - - -
52F THR* 1.3 83.5 + - - +
54F HIS* 1.3 79.4 + - - +
55F ASP* 4.5 0.7 - - - -
57F ASP* 4.3 0.9 - - + +
58F LEU* 3.7 29.4 - - + -
75F PHE* 5.0 6.3 - + - -
86F VAL* 3.4 31.0 - - + -
88F MET* 3.7 2.7 + - - -
89F ALA* 3.6 21.1 - - + +
90F THR* 3.0 26.2 + - - +
122F ASN* 4.1 22.4 - - - -
125F LEU* 4.5 5.6 - - + -
126F ALA* 4.9 3.4 - - - -
129F LEU* 3.5 24.0 - - + -
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Residues in contact with HIS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F TRP* 3.1 58.5 - + - +
53F PHE* 1.3 84.9 - - - +
55F ASP* 1.3 70.5 + - - +
56F ASP 4.1 4.0 - - - +
57F ASP* 2.9 36.6 + - - +
58F LEU 3.6 0.2 + - - -
90F THR* 3.4 26.8 + - + +
91F THR 3.7 17.0 + - - -
92F ASN* 3.9 8.5 - - + +
94F PHE* 3.7 29.4 - + - -
137F 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