Contacts of the helix formed by residues 140 - 151 (chain C) in PDB entry 3P71
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 ALA 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C TYR* 4.0 30.5 - - + +
133C CYS* 5.8 0.2 - - - -
134C LEU* 4.3 4.8 - - + +
139C ASN* 1.3 73.7 - - - +
141C ASN* 1.3 55.1 + - - +
142C VAL 3.3 3.1 - - - -
143C TRP* 3.2 15.8 + - + +
144C LYS* 2.8 36.2 + - + +
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Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.3 20.1 + - - +
139C ASN* 2.9 26.1 + - - +
140C ALA* 1.3 76.6 + - - +
142C VAL* 1.3 56.5 + - - +
144C LYS* 3.1 21.6 - - - +
145C TYR* 2.8 58.4 + - + +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.8 20.4 - - + -
28C VAL* 4.2 11.2 - - + -
94C VAL* 5.2 1.3 - - + -
133C CYS* 4.1 12.1 - - + -
137C TYR* 3.7 57.0 - - + +
139C ASN* 4.4 2.0 + - - +
140C ALA 3.3 0.6 - - - -
141C ASN* 1.3 72.7 - - - +
143C TRP* 1.3 68.2 + - - +
145C TYR* 3.0 17.0 + - + +
146C PHE* 3.0 40.8 + - + -
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Residues in contact with TRP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ARG* 3.6 47.3 - - + -
124C THR* 2.9 21.2 + - - -
125C GLN* 3.9 19.3 - - + -
129C PHE* 3.6 27.8 - + - -
130C TYR* 3.7 43.0 - + + +
133C CYS* 3.9 22.4 - - + +
140C ALA* 3.2 17.1 + - + +
142C VAL* 1.3 77.5 - - - +
144C LYS* 1.3 76.7 + - + +
146C PHE* 3.4 0.9 + - - +
147C THR* 2.6 44.9 + - + +
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Residues in contact with LYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ARG* 5.9 1.1 - - - +
140C ALA* 2.8 16.8 + - + +
141C ASN* 3.1 26.1 - - - +
143C TRP* 1.3 85.1 - - + +
145C TYR* 1.3 81.8 + - + +
147C THR* 3.1 7.0 + - - -
148C ASP* 3.0 53.8 + - - +
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 4.2 13.2 + - + -
28C VAL* 4.4 6.3 - - + -
29C LYS* 3.8 52.9 - - + +
32C CYS* 3.7 26.1 - - + +
36C LYS* 5.1 1.7 - - - -
141C ASN* 2.8 54.0 + - + -
142C VAL* 3.0 9.8 + - - +
144C LYS* 1.3 99.5 + - + +
146C PHE* 1.3 63.2 + - - +
148C ASP* 3.7 7.1 + - - +
149C LEU* 3.3 20.1 + - - +
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.5 27.4 - - + -
31C LEU* 5.4 2.0 - - + -
32C CYS* 4.1 13.7 - - - -
94C VAL* 5.0 3.6 - - + -
97C VAL* 3.7 39.9 - - + -
98C THR* 3.2 33.7 - - + -
101C VAL* 4.3 9.6 - - + -
129C PHE* 4.0 19.1 - + + -
142C VAL* 3.0 37.2 + - + +
143C TRP 4.1 0.2 - - - +
145C TYR* 1.3 73.9 - - - +
147C THR* 1.3 59.6 - - - +
149C LEU* 2.9 26.6 + - + +
150C PHE* 3.0 35.4 + + + -
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 4.9 0.5 + - - -
120C SER 4.6 0.2 - - - +
121C ARG* 3.2 43.3 + - + +
124C THR* 4.1 7.9 - - - +
129C PHE* 4.7 1.6 - - + -
143C TRP* 2.6 62.0 + - + +
144C LYS* 3.1 13.0 + - - -
146C PHE* 1.3 72.8 - - - +
148C ASP* 1.3 63.9 + - - +
149C LEU 3.4 0.3 + - - -
150C PHE* 3.5 30.9 + - + +
151C ASP* 3.8 5.7 - - - +
188C GLU* 5.6 0.2 - - - +
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Residues in contact with ASP 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS* 4.4 19.5 + - - +
121C ARG* 2.8 33.6 + - - +
144C LYS* 3.0 44.4 + - - +
145C TYR* 3.8 9.1 - - - +
147C THR* 1.3 77.1 - - - +
149C LEU* 1.3 60.3 + - - +
151C ASP* 3.7 8.8 - - - +
152C TYR* 3.5 21.5 - - - -
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C CYS* 3.6 29.6 - - + +
35C ALA* 3.7 10.1 - - + -
36C LYS* 3.8 14.6 - - + +
39C LEU* 3.7 27.4 - - + -
101C VAL* 3.8 35.4 - - + -
113C ILE* 6.1 0.2 - - + -
145C TYR 3.3 11.5 + - - +
146C PHE* 2.9 21.2 + - + +
148C ASP* 1.3 77.1 - - - +
150C PHE* 1.3 65.4 + - + +
151C ASP 3.1 2.5 - - - -
152C TYR* 2.9 28.9 + - + +
153C LEU* 3.6 8.9 + - + +
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Residues in contact with PHE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 5.5 0.7 - + - -
87C VAL* 4.4 16.2 - - + -
97C VAL* 4.1 25.6 - - + -
115C ARG* 2.9 28.6 + - - +
118C HIS 4.7 0.4 - - - -
119C GLU* 3.5 61.5 - - + +
120C SER* 4.0 2.5 - - - -
124C THR* 4.8 1.1 - - + -
129C PHE* 4.4 8.3 - + - -
146C PHE* 3.0 41.9 + + + -
147C THR* 3.7 23.6 - - + +
148C ASP 3.5 0.6 - - - -
149C LEU* 1.3 80.5 - - + +
151C ASP* 1.3 62.1 + - - +
152C TYR 3.1 0.9 + - - -
153C LEU* 3.2 23.0 + - + +
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Residues in contact with ASP 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 2.9 27.0 + - - +
121C ARG* 2.8 32.5 + - - -
147C THR 3.8 1.2 - - - +
148C ASP 3.7 11.2 - - - +
149C LEU 3.1 0.4 - - - -
150C PHE* 1.3 76.7 - - - +
152C TYR* 1.3 65.2 + - + +
153C LEU 3.5 1.0 - - - +
185C ARG* 3.0 25.6 - - - +
186C LEU* 3.4 11.3 + - + +
187C GLN* 3.2 32.3 - - - +
188C GLU* 3.6 2.9 + - - +
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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