Contacts of the helix formed by residues 140 - 152 (chain F) in PDB entry 5IRC
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 LYS 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122F ARG* 3.7 2.9 - - - +
128F ARG* 6.3 0.9 - - - +
137F GLU* 2.6 32.9 + - - -
138F PRO 4.3 6.7 - - - +
139F VAL* 1.3 78.2 - - - +
141F PRO* 1.3 75.8 - - + +
142F GLU* 3.3 29.8 - - + +
143F GLU* 2.7 43.2 + - - +
144F GLY* 3.1 9.9 + - - -
158F GLU* 4.5 0.2 - - - +
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Residues in contact with PRO 141 (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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122F ARG* 3.4 33.8 - - - +
140F LYS* 1.3 87.1 - - + +
142F GLU* 1.3 64.6 + - - +
144F GLY* 3.2 2.3 + - - -
145F ARG* 2.9 29.6 + - - +
156F TYR* 3.8 5.3 - - + -
158F GLU* 3.4 20.9 - - - +
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Residues in contact with GLU 142 (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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140F LYS* 3.3 32.3 - - + +
141F PRO* 1.3 88.4 - - - +
143F GLU* 1.3 64.2 + - + +
145F ARG* 3.4 5.5 + - - +
146F ASP* 2.8 43.4 + - - +
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Residues in contact with GLU 143 (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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92F LEU* 4.3 12.0 - - + +
137F GLU* 4.9 1.4 - - - +
138F PRO 4.4 1.2 - - - +
139F VAL* 3.6 15.6 - - + +
140F LYS* 2.7 60.3 + - + +
142F GLU* 1.3 79.5 - - + +
144F GLY* 1.3 64.7 + - - +
146F ASP* 3.8 7.9 - - - +
147F MET* 3.1 23.4 + - - +
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Residues in contact with GLY 144 (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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84F PHE* 4.3 12.1 - - - -
92F LEU* 4.9 0.9 - - - -
114F LEU* 3.7 6.4 - - - +
139F VAL* 4.1 2.5 - - - +
140F LYS 3.1 10.3 + - - -
141F PRO 3.2 0.4 + - - -
143F GLU* 1.3 76.9 - - - +
145F ARG* 1.3 62.2 + - - +
147F MET* 3.1 8.0 + - - +
148F ALA 3.0 18.4 + - - -
156F TYR* 3.4 30.3 - - - -
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Residues in contact with ARG 145 (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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141F PRO 2.9 15.9 + - - +
142F GLU* 3.8 6.3 - - - +
144F GLY* 1.3 74.2 - - - +
146F ASP* 1.3 60.6 + - - +
148F ALA* 3.1 4.3 + - - +
149F ASN* 2.9 47.3 + - - +
155F GLY* 5.8 1.2 - - - -
156F TYR* 3.4 61.4 + - + +
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Residues in contact with ASP 146 (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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142F GLU* 2.8 34.3 + - - +
143F GLU* 3.8 7.6 - - - +
145F ARG* 1.3 75.4 - - - +
147F MET* 1.3 58.3 + - - +
149F ASN* 3.4 15.1 + - - +
150F ARG* 2.9 28.5 + - - +
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Residues in contact with MET 147 (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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92F LEU* 3.9 30.5 - - + +
93F GLU* 5.3 2.0 - - - -
95F ILE* 3.8 22.7 - - + -
96F PRO* 3.6 39.3 - - + -
114F LEU* 4.0 7.0 - - + -
143F GLU 3.1 12.9 + - - +
144F GLY 3.1 9.6 + - - +
146F ASP* 1.3 74.2 - - - +
148F ALA* 1.3 66.0 + - - +
150F ARG* 3.1 23.0 + - - +
151F ILE* 3.0 27.1 + - + +
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Residues in contact with ALA 148 (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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114F LEU* 3.5 16.0 - - + +
144F GLY 3.0 8.9 + - - +
145F ARG* 3.4 9.2 - - - +
147F MET* 1.3 75.7 - - - +
149F ASN* 1.3 66.0 + - - +
151F ILE* 3.4 1.5 + - - +
152F GLY 3.2 3.5 + - - -
153F ALA* 3.0 44.1 + - + +
155F GLY 4.4 1.1 - - - +
156F TYR* 3.6 30.1 - - + +
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Residues in contact with ASN 149 (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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1250B PRO* 3.1 25.0 - - + +
145F ARG* 2.9 40.0 + - - +
146F ASP* 3.5 16.2 + - - +
148F ALA* 1.3 78.8 - - - +
150F ARG* 1.3 62.2 + - - +
152F GLY* 3.2 8.2 + - - -
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Residues in contact with ARG 150 (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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1243B GLU* 5.9 0.4 - - - +
1244B SER* 3.0 33.7 + - - +
1245B ASN* 3.2 18.4 + - - -
1247B PHE 4.5 3.0 + - - -
1248B GLY* 3.8 16.2 + - - +
1249B VAL* 3.7 19.3 - - + +
1250B PRO* 3.7 9.3 - - - +
1329B PRO* 3.3 23.2 - - - +
96F PRO* 5.2 7.9 - - - -
146F ASP 2.9 19.2 + - - +
147F MET* 3.1 26.4 + - - +
149F ASN* 1.3 77.2 - - - +
151F ILE* 1.3 63.0 + - + +
152F GLY 3.3 0.2 - - - -
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Residues in contact with ILE 151 (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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1329B PRO* 4.0 3.1 - - - -
82F MET* 4.0 12.3 - - + -
95F ILE* 4.0 17.0 - - + -
96F PRO* 4.8 7.4 - - + -
100F THR* 3.6 38.4 - - + +
104F LYS* 2.7 33.4 + - - +
112F ILE* 4.6 9.7 - - + +
114F LEU* 4.4 10.5 - - + -
147F MET* 3.0 34.5 + - - +
148F ALA 3.6 7.2 - - - +
150F ARG* 1.3 79.4 - - + +
152F GLY* 1.3 58.8 + - - +
153F ALA* 3.8 16.8 - - + +
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Residues in contact with GLY 152 (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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1250B PRO* 4.9 4.0 - - - -
1329B PRO* 4.1 10.9 - - - +
1330B ASP* 4.4 15.9 - - - +
104F LYS* 5.2 1.2 + - - -
112F ILE* 5.6 2.5 + - - +
148F ALA 3.8 0.4 - - - -
149F ASN 3.2 14.7 + - - -
150F ARG 3.3 1.4 + - - -
151F ILE* 1.3 80.8 - - - +
153F ALA* 1.3 67.4 + - - +
154F PHE 3.7 0.5 + - - -
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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