Contacts of the helix formed by residues 73 - 80 (chain B) in PDB entry 1FA0
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 SER 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 5.2 6.5 - - - +
161A ASP* 2.8 36.4 + - - -
179A ASN* 3.6 20.9 + - - -
68B LYS* 3.9 1.3 - - - +
71B ASN 4.3 0.2 + - - -
72B MET* 1.3 78.4 - - - +
74B ASP* 1.3 58.8 + - - +
75B GLY 3.4 2.5 + - - -
76B MET* 3.0 17.5 + - - +
77B ALA* 2.8 26.7 + - - +
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 2.6 29.3 + - - +
68B LYS* 2.6 27.2 + - - +
73B SER* 1.3 74.3 - - - +
75B GLY* 1.3 59.2 + - - +
77B ALA* 3.7 3.2 - - - +
78B ARG* 2.9 44.2 + - - +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG* 3.5 25.3 + - - -
179A ASN* 5.1 1.6 - - - +
73B SER* 3.1 4.3 + - - -
74B ASP* 1.3 78.2 - - - +
76B MET* 1.3 59.5 + - - +
78B ARG* 3.5 19.7 + - - +
79B ASP* 3.0 34.5 + - - +
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 4.0 27.1 - - + -
161A ASP* 3.9 24.2 - - - +
162A GLN* 3.9 15.0 - - - -
163A PRO* 4.2 27.1 - - + -
178A ARG* 3.5 6.6 - - - +
72B MET* 3.3 51.5 - - + +
73B SER* 3.0 20.5 + - - +
75B GLY* 1.3 75.3 - - - +
77B ALA* 1.3 59.6 + - - +
79B ASP* 3.0 4.0 + - + +
80B ALA* 2.9 26.0 + - - -
164B GLN* 5.2 1.7 - - - +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.6 39.5 + - + +
67B SER* 3.5 27.3 + - - -
68B LYS* 4.0 12.6 - - + +
72B MET* 3.8 3.3 - - + +
73B SER 2.8 17.8 + - - +
74B ASP 3.7 5.6 - - - +
76B MET* 1.3 79.2 - - - +
78B ARG* 1.3 58.3 + - - +
80B ALA* 3.8 11.0 - - - +
81B GLY 4.5 1.6 + - - +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG* 4.9 3.4 - - - +
64B TYR* 3.9 16.7 - - + -
74B ASP* 2.9 36.0 + - - +
75B GLY* 3.5 18.0 + - - +
76B MET 3.1 0.2 - - - -
77B ALA* 1.3 77.4 - - - +
79B ASP* 1.3 69.7 + - - +
80B ALA 3.2 0.2 - - - -
81B GLY* 3.2 13.9 + - - -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLN* 5.9 0.3 - - - +
178A ARG* 3.1 32.7 + - - +
75B GLY 3.0 18.2 + - - +
76B MET* 3.0 6.5 + - - +
78B ARG* 1.3 81.7 + - - +
80B ALA* 1.3 60.2 + - - +
81B GLY* 2.9 8.2 + - - -
164B GLN* 3.5 37.5 + - - +
165B VAL 4.5 2.6 + - - -
166B PRO* 5.1 3.1 - - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 3.6 11.9 - - + -
67B SER* 3.4 25.6 - - - +
72B MET* 4.6 2.9 - - + -
76B MET 2.9 13.2 + - - +
77B ALA 3.8 3.1 - - - +
78B ARG 3.2 0.2 - - - -
79B ASP* 1.3 76.1 - - - +
81B GLY* 1.3 61.3 + - - +
82B GLY 3.6 0.5 + - - -
108B PRO* 3.8 9.3 - - + +
110B HIS* 3.9 16.8 - - + +
163B PRO 4.2 1.6 - - - +
164B GLN* 3.7 14.7 - - - +
165B VAL* 3.0 21.4 + - - -
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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