Contacts of the helix formed by residues 79 - 88 (chain A) in PDB entry 1R9F
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 THR 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 2.6 36.7 + - - +
78A ARG* 1.3 83.9 - - - +
80A GLU* 1.3 59.5 + - - +
81A ALA* 3.8 7.7 + - - +
82A SER* 3.2 14.8 + - - -
83A LEU* 2.9 29.0 + - - +
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Residues in contact with GLU 80 (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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78A ARG 4.2 0.2 + - - -
79A THR* 1.3 73.7 - - - +
81A ALA* 1.3 62.7 + - - +
83A LEU* 3.4 8.8 + - - +
84A HIS* 3.0 24.4 + - - +
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Residues in contact with ALA 81 (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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79A THR* 3.2 8.2 + - - +
80A GLU* 1.3 79.5 - - - +
82A SER* 1.3 61.0 - - - +
84A HIS* 3.3 6.6 + - - +
85A ARG* 3.0 22.9 + - - +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 3.9 4.7 + - - -
76A TYR* 3.3 16.7 - - - -
77A ASP* 2.9 46.6 + - - -
79A THR* 3.2 7.3 + - - -
81A ALA* 1.3 77.5 - - - +
83A LEU* 1.3 65.8 + - - +
85A ARG* 3.2 12.0 + - - +
86A VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 83 (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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76A TYR* 3.6 16.5 - - + +
79A THR 2.9 17.8 + - - +
80A GLU* 3.8 8.5 - - - +
81A ALA 3.3 0.2 - - - -
82A SER* 1.3 76.6 - - - +
84A HIS* 1.3 63.1 - - - +
86A VAL* 3.4 1.9 - - - +
87A LEU* 3.0 51.6 + - + +
142A GLN* 4.9 4.5 - - - +
145A LEU* 3.8 38.6 - - + -
146A GLN* 3.6 37.2 - - + +
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Residues in contact with HIS 84 (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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80A GLU 3.0 17.2 + - - +
81A ALA* 3.5 7.2 - - - +
83A LEU* 1.3 79.7 - - - +
85A ARG* 1.3 68.3 + - - +
87A LEU* 3.5 13.7 + - - +
88A GLY* 3.5 7.4 + - - -
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Residues in contact with ARG 85 (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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32A LEU* 3.7 32.0 - - + +
35A GLU* 2.9 38.9 + - - -
74A LEU* 4.5 1.6 - - - +
75A ARG* 2.9 32.3 + - - +
81A ALA 3.0 13.6 + - - +
82A SER* 3.2 12.6 + - - +
84A HIS* 1.3 82.2 - - + +
86A VAL* 1.3 71.4 + - - +
88A GLY* 3.1 19.8 + - - -
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Residues in contact with VAL 86 (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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32A LEU* 4.7 2.2 - - - -
59A PHE* 3.8 21.5 - - + -
74A LEU* 4.2 10.3 - - + -
75A ARG 3.4 26.0 - - - +
76A TYR* 4.1 6.5 - - + -
82A SER 3.0 19.1 + - - +
83A LEU* 3.4 9.9 - - - +
85A ARG* 1.3 85.2 - - - +
87A LEU* 1.3 61.5 + - - +
88A GLY 2.9 6.1 - - - -
89A SER* 3.0 11.1 + - - +
141A LYS* 2.8 21.9 + - - -
145A LEU* 3.6 29.4 - - + -
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Residues in contact with LEU 87 (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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83A LEU* 3.0 49.3 + - + +
84A HIS* 3.9 7.9 - - - +
85A ARG 3.3 0.4 - - - -
86A VAL* 1.3 76.4 - - - +
88A GLY* 1.3 58.5 + - - +
89A SER 3.3 1.8 + - - -
90A TRP 3.6 13.5 + - - +
91A THR* 5.7 0.5 - - - +
138A ILE* 4.2 23.4 - - + +
141A LYS* 4.0 32.1 + - + +
142A GLN* 4.2 36.8 - - + +
145A LEU* 4.8 0.7 - - + -
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Residues in contact with GLY 88 (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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31A LYS* 3.8 21.0 + - - +
32A LEU* 4.4 6.0 - - - +
84A HIS 3.5 5.9 + - - -
85A ARG 3.1 12.9 + - - -
86A VAL 2.9 1.8 - - - -
87A LEU* 1.3 78.1 - - - +
89A SER* 1.3 62.4 + - - +
90A TRP 3.1 5.6 + - - -
91A THR* 5.2 3.7 - - - +
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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