Contacts of the helix formed by residues 136 - 143 (chain I) in PDB entry 1FQV
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 CYS 136 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ASP* 4.7 4.3 - - - -
133I SER 4.1 0.2 - - - +
135I VAL* 1.3 80.6 - - - +
137I LYS* 1.3 63.8 + - - +
138I ARG* 3.0 12.7 + - - -
139I TRP* 3.1 45.5 + - - +
140I TYR 3.0 17.3 + - - -
141J ILE* 3.8 16.4 - - + -
142J LYS 3.7 13.2 - - - +
144J ASP* 3.1 20.9 - - - +
145J PHE* 3.4 13.4 - - - -
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Residues in contact with LYS 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I CYS* 1.3 73.6 - - - +
138I ARG* 1.3 60.7 + - - +
140I TYR* 3.5 4.5 + - - +
141I ARG* 3.2 28.2 + - + +
144J ASP* 3.0 38.0 + - + +
145J PHE* 3.6 22.5 - - + -
146J THR* 4.8 1.8 + - - -
149J GLU* 2.9 44.1 + - - -
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Residues in contact with ARG 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ASP* 2.8 52.4 + - - +
112I LEU 2.6 27.1 + - - +
113I PRO* 3.4 0.8 + - - +
114I ASP* 2.5 45.8 + - - +
117I LEU* 3.4 25.3 - - - +
136I CYS* 3.0 10.2 + - - -
137I LYS* 1.3 76.7 - - - +
139I TRP* 1.3 66.5 + - - +
141I ARG* 3.0 37.1 + - - +
142I LEU* 3.0 18.3 + - + +
144J ASP* 4.1 3.6 + - - +
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Residues in contact with TRP 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I TRP* 5.4 6.1 - - + -
110I ASP* 4.9 6.1 + - - +
117I LEU* 3.5 42.7 - - + +
120I ILE* 6.1 0.9 - - + -
121I PHE* 3.4 25.4 - + + -
132I VAL* 3.5 21.1 - - + +
133I SER* 4.2 1.3 - - - -
135I VAL* 3.5 32.1 - - + -
136I CYS* 3.1 28.5 + - - +
138I ARG* 1.3 82.4 - - + +
140I TYR* 1.3 53.1 + - - +
142I LEU* 4.6 1.6 - - - -
143I ALA* 2.7 39.7 + - - +
123J VAL* 6.1 1.3 - - + -
127J ILE* 3.8 30.5 - - + -
135J ILE* 4.1 15.7 - - + -
139J PHE* 4.3 11.2 - + - -
141J ILE* 4.8 20.8 - - + +
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Residues in contact with TYR 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I SER* 2.9 36.1 + - - +
136I CYS 3.0 9.3 + - - +
137I LYS* 3.5 11.0 - - - +
138I ARG 3.1 0.2 - - - -
139I TRP* 1.3 76.0 - - - +
141I ARG* 1.3 74.3 + - + +
143I ALA* 3.6 4.0 + - - +
144I SER* 3.6 22.4 + - - -
145J PHE* 3.8 9.4 - + + -
152J GLN* 5.3 1.5 + - - -
153J VAL* 3.6 29.6 - - + -
156J GLU* 3.0 40.0 + - + -
157J ASN* 5.8 0.7 - - - -
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Residues in contact with ARG 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I ASP* 3.8 20.2 + - - -
137I LYS* 3.2 16.0 + - + +
138I ARG* 3.0 34.2 + - - +
140I TYR* 1.3 86.5 - - + +
142I LEU* 1.3 76.3 + - - +
144I SER* 3.1 16.0 + - - -
145I ASP* 3.7 4.2 + - - -
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Residues in contact with LEU 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I ASP* 3.4 30.7 - - + +
117I LEU* 3.5 41.5 - - + -
118I LEU* 3.7 23.2 - - + +
121I PHE* 3.9 9.6 - - + -
138I ARG* 3.0 28.1 + - - +
139I TRP 3.9 2.2 - - - +
141I ARG* 1.3 88.5 - - - +
143I ALA* 1.3 54.7 + - - +
144I SER 2.8 5.4 - - - -
145I ASP* 2.7 38.8 + - - +
148I LEU* 3.3 7.4 - - - +
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Residues in contact with ALA 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I PHE* 3.8 14.1 - - + -
129I LEU* 3.7 30.2 - - + +
130I LEU* 5.8 1.2 - - + +
133I SER* 3.5 31.4 - - - +
139I TRP 2.7 23.2 + - - +
140I TYR 4.0 2.5 - - - +
141I ARG 3.3 0.4 - - - -
142I LEU* 1.3 71.5 - - - +
144I SER* 1.3 58.5 + - - +
145I ASP 3.5 0.2 - - - -
148I LEU* 3.9 1.9 - - - +
149I TRP* 2.9 20.4 + - - -
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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