Contacts of the helix formed by residues 123 - 132 (chain B) in PDB entry 1FR2
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU 4.7 1.6 - - - +
26B ALA 3.0 4.9 + - - -
27B GLY* 3.6 16.7 - - - +
87B THR* 4.1 2.7 - - + -
88B PRO* 5.5 0.7 - - + -
91B GLN* 2.7 46.8 + - + +
99B TYR* 3.6 26.2 - - + +
100B GLU* 5.1 0.7 - - - -
122B THR* 1.3 75.2 - - - +
124B PRO* 1.3 76.9 - - - +
125B LYS 3.8 0.2 + - - -
126B ARG* 3.2 15.6 + - - +
127B HIS* 2.8 21.5 + - - +
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Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 3.7 11.4 - - + +
91B GLN 3.3 14.6 - - - +
92B GLN* 4.5 0.2 - - - -
93B VAL* 4.0 9.9 - - + +
96B ARG* 3.3 43.5 - - + +
97B LYS* 4.2 1.8 - - - +
98B VAL 3.3 26.9 - - - +
100B GLU* 3.7 18.8 - - - +
123B THR* 1.3 83.7 - - - +
125B LYS* 1.3 63.1 + - - +
127B HIS* 3.6 1.0 - - - +
128B ILE* 3.0 29.3 + - - +
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Residues in contact with LYS 125 (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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90B ASN 3.7 20.2 + - - +
91B GLN* 3.1 37.4 + - - +
92B GLN 5.1 0.7 - - - +
93B VAL* 3.7 16.3 - - + +
123B THR 3.2 0.2 - - - -
124B PRO* 1.3 80.2 - - - +
126B ARG* 1.3 62.0 + - - +
128B ILE* 3.6 3.1 + - - +
129B ASP* 3.1 37.6 + - - +
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Residues in contact with ARG 126 (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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26B ALA 3.7 14.4 - - - +
27B GLY 3.6 29.2 - - - +
28B LYS* 3.9 3.8 - - - +
29B ASP* 2.7 37.6 + - - +
91B GLN* 4.7 0.2 - - - +
122B THR* 4.7 1.3 - - + -
123B THR* 3.2 18.0 + - - +
125B LYS* 1.3 78.4 - - - +
127B HIS* 1.3 60.7 - - - +
129B ASP* 3.7 26.9 + - - +
130B ILE* 2.8 56.3 + - + +
132B ARG* 5.5 4.9 - - - +
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Residues in contact with HIS 127 (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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96B ARG* 4.0 6.6 + - - +
100B GLU* 2.7 32.7 + - + +
101B LEU 3.8 19.3 - - - -
102B HIS* 3.2 15.9 + + + +
122B THR* 3.3 18.6 - - + +
123B THR 2.8 12.9 + - - +
124B PRO 3.6 1.3 - - - +
126B ARG* 1.3 77.2 - - - +
128B ILE* 1.3 63.2 + - - +
130B ILE* 3.3 4.6 + - + +
131B HIS* 3.2 30.2 + + - -
301B ZN 2.0 37.5 - - - -
403B PO4 3.9 11.0 - - - -
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Residues in contact with ILE 128 (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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93B VAL* 3.7 36.8 - - + -
96B ARG* 3.6 33.4 - - - +
124B PRO 3.0 20.2 + - - +
125B LYS 3.8 3.6 - - - +
127B HIS* 1.3 77.2 - - - +
129B ASP* 1.3 69.6 + - - +
131B HIS* 3.5 5.9 + - - +
132B ARG 3.1 24.6 + - - +
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Residues in contact with ASP 129 (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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125B LYS* 3.1 36.4 + - - +
126B ARG* 3.7 27.1 + - - +
127B HIS 3.2 0.2 - - - -
128B ILE* 1.3 82.9 - - - +
130B ILE* 1.3 61.2 + - - +
132B ARG* 2.9 44.5 + - - +
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Residues in contact with ILE 130 (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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29B ASP 3.6 25.6 - - - +
30B SER* 3.9 21.3 - - - +
102B HIS* 3.6 31.4 - - + +
122B THR* 4.0 15.9 - - + -
126B ARG* 2.8 44.1 + - + +
127B HIS* 3.3 5.8 + - - +
129B ASP* 1.3 73.1 - - - +
131B HIS* 1.3 60.5 + - - +
132B ARG* 2.9 20.7 - - - +
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Residues in contact with HIS 131 (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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102B HIS* 3.2 12.7 + + - -
103B HIS 5.3 1.3 - - - -
106B PRO* 5.9 9.2 - - + -
127B HIS* 3.2 31.7 + + - +
128B ILE* 4.0 4.5 - - - +
130B ILE* 1.3 75.1 - - - +
132B ARG* 1.3 76.0 + - - +
301B ZN 2.0 37.5 - - - -
403B PO4 3.8 11.7 + - - -
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Residues in contact with ARG 132 (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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126B ARG* 5.5 5.1 - - - +
128B ILE* 3.1 17.0 + - - +
129B ASP* 2.9 37.9 + - - +
130B ILE* 2.9 20.5 - - - +
131B HIS* 1.3 86.1 - - - +
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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