Contacts of the helix formed by residues 136 - 142 (chain A) in PDB entry 3PEP
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 VAL 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.1 25.5 - - + +
89A VAL* 5.5 4.0 - - + -
91A VAL* 4.8 13.7 - - + -
96A ASP* 3.9 8.7 - - - +
99A GLN* 3.4 26.1 - - + +
121A LEU* 4.0 33.4 - - + -
122A GLY 5.0 3.0 + - - +
123A LEU* 5.6 3.1 - - + -
134A THR 3.5 3.6 + - - -
135A PRO* 1.3 68.1 - - - +
137A PHE* 1.3 67.2 + - + +
139A ASN* 2.9 6.4 + - - +
140A LEU* 2.8 39.0 + - + +
167A LEU* 5.8 2.5 - - + -
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Residues in contact with PHE 137 (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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122A GLY 5.6 0.8 + - - -
123A LEU* 4.6 14.3 - - + +
135A PRO* 3.2 2.8 + - + +
136A VAL* 1.3 80.7 - - - +
138A ASP* 1.3 60.7 - - - +
140A LEU* 2.8 36.9 + - + +
141A TRP* 2.9 13.4 + - + +
146A VAL* 4.5 17.7 - - + -
148A GLN 4.1 2.9 - - - -
149A ASP* 3.6 32.8 - - - -
150A LEU 3.5 32.3 - - - -
151A PHE* 3.8 40.2 - + + -
167A LEU* 4.8 7.9 - - + -
168A GLY 4.3 9.0 - - - -
315A ARG* 4.0 18.6 - - + +
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Residues in contact with ASP 138 (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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124A ALA 4.9 0.5 - - - +
126A PRO* 3.3 20.8 - - - +
134A THR* 4.1 7.9 - - + -
135A PRO* 2.8 40.4 + - + +
137A PHE* 1.3 80.3 - - - +
139A ASN* 1.3 54.7 + - - +
141A TRP* 3.5 6.5 + - - +
142A ASP* 2.9 42.7 + - - +
315A ARG* 2.9 31.5 + - - +
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Residues in contact with ASN 139 (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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96A ASP* 3.6 4.3 + - - +
97A THR 3.4 4.0 + - - -
98A ASN* 3.2 24.3 + - - +
99A GLN* 3.1 33.8 + - - +
100A ILE 5.8 0.2 - - - -
134A THR* 4.1 16.9 - - + +
135A PRO 3.1 6.3 + - - +
136A VAL 2.9 3.8 + - - +
138A ASP* 1.3 73.5 - - - +
140A LEU* 1.3 64.3 + - - +
142A ASP* 3.8 8.9 + - - +
143A GLN* 3.0 55.6 + - - +
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Residues in contact with LEU 140 (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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91A VAL* 4.7 3.4 - - + -
94A ILE* 3.6 38.6 - - + -
96A ASP* 3.8 19.1 - - + +
136A VAL* 2.8 31.5 + - + +
137A PHE* 2.8 20.2 + - + +
139A ASN* 1.3 76.9 - - - +
141A TRP* 1.3 60.0 + - - +
143A GLN* 3.2 2.9 + - - -
144A GLY 3.1 3.5 + - - -
145A LEU* 3.0 39.4 + - + +
146A VAL* 4.3 15.3 - - + -
167A LEU* 4.1 29.8 - - + -
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Residues in contact with TRP 141 (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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137A PHE* 2.9 12.2 + - + +
138A ASP* 3.8 9.4 - - - +
140A LEU* 1.3 75.1 - - - +
142A ASP* 1.3 67.0 + - - +
144A GLY* 2.9 21.0 + - - -
146A VAL* 3.8 32.1 - - + +
147A SER 3.6 23.1 - - - -
148A GLN 3.9 0.4 - - - -
149A ASP* 3.3 56.8 + - + +
316A ALA* 5.7 1.6 - - + -
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Residues in contact with ASP 142 (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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134A THR* 4.5 8.7 - - - +
138A ASP* 2.9 35.4 + - - +
139A ASN* 4.2 13.1 + - - +
140A LEU 3.4 0.2 - - - -
141A TRP* 1.3 85.0 - - - +
143A GLN* 1.3 60.9 + - + +
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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