Contacts of the helix formed by residues 137 - 149 (chain F) in PDB entry 3PJV
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 PRO 137 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.9 26.2 - - + -
77D SER* 4.3 3.1 - - - +
97D PRO 4.0 13.7 - - - +
99D VAL* 5.6 1.3 - - + -
112F LEU* 4.1 12.1 - - + -
135F SER 3.5 6.3 - - - +
136F HIS* 1.3 95.4 - - + +
138F MSE 1.3 63.7 + - - +
139F PHE 3.2 3.0 + - - -
140F ALA* 3.2 3.8 + - - +
141F LEU* 3.0 40.5 + - + +
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Residues in contact with MSE 138 (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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99D VAL* 4.1 21.4 - - + +
100D THR* 3.6 43.1 - - - +
138D MSE 3.6 38.7 - - + +
139D PHE* 3.2 44.4 - - + -
142D ALA* 4.3 8.1 - - + -
100F THR* 4.6 7.9 - - + +
136F HIS* 3.0 23.3 + - + +
137F PRO* 1.3 77.8 - - - +
139F PHE* 1.3 57.3 + - - +
141F LEU* 3.4 2.3 + - - +
142F ALA* 3.0 29.3 + - - +
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Residues in contact with PHE 139 (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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136D HIS* 3.6 36.3 - + + -
138D MSE 3.7 21.8 - - + -
139D PHE* 3.8 16.2 - + + -
74F GLY 4.1 7.4 - - - -
75F TYR* 3.3 55.0 - + + +
76F TYR 4.4 7.0 - - - -
96F ILE* 3.9 17.0 - - + -
136F HIS 4.6 0.6 + - - +
137F PRO 3.3 0.8 - - - -
138F MSE 1.3 78.2 - - - +
140F ALA* 1.3 66.5 + - - +
142F ALA* 3.2 3.2 + - - +
143F LYS* 3.0 47.6 + - + +
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Residues in contact with ALA 140 (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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34D TYR* 4.0 30.2 - - + -
37D GLN* 5.8 1.6 - - - +
38D LEU* 3.9 34.3 - - + +
75F TYR* 5.4 0.6 - - - -
112F LEU* 4.8 4.9 - - + -
137F PRO* 3.2 8.4 + - - +
139F PHE* 1.3 78.5 - - - +
141F LEU* 1.3 58.2 + - - +
143F LYS* 3.2 4.2 + - - +
144F LEU* 2.9 32.5 + - + +
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Residues in contact with LEU 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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99D VAL* 3.8 26.2 - - + -
102F VAL* 4.4 11.1 - - + +
106F PHE* 4.4 5.6 - - + -
107F VAL* 4.2 30.1 - - + +
110F ILE* 4.2 27.8 - - + -
112F LEU* 3.8 24.5 - - + +
137F PRO* 3.0 35.4 + - + +
138F MSE 3.8 3.8 - - - +
140F ALA* 1.3 76.9 - - - +
142F ALA* 1.3 58.4 + - - +
144F LEU* 3.3 7.6 + - + +
145F TRP* 2.9 30.7 + - - +
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Residues in contact with ALA 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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138D MSE 3.8 13.2 - - + -
96F ILE* 3.6 20.4 - - + -
100F THR* 3.9 24.7 - - - +
102F VAL* 5.1 1.7 - - - +
138F MSE 3.0 19.2 + - - +
139F PHE 3.6 4.9 - - - +
141F LEU* 1.3 76.9 - - - +
143F LYS* 1.3 57.7 + - - +
145F TRP* 3.4 5.0 + - - +
146F GLN* 3.0 33.8 + - + +
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Residues in contact with LYS 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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34D TYR* 3.5 34.4 + - + +
37D GLN* 4.8 5.9 + - - +
71F PHE 5.6 0.6 + - - -
72F ASP* 4.1 27.3 + - - +
74F GLY 6.0 0.2 + - - -
96F ILE* 4.1 15.9 - - + -
139F PHE* 3.0 43.1 + - + +
140F ALA* 3.5 8.3 - - - +
141F LEU 3.2 0.2 - - - -
142F ALA* 1.3 75.2 - - - +
144F LEU* 1.3 65.2 + - - +
146F GLN* 3.3 6.7 + - - +
147F SER* 3.0 27.2 + - - -
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Residues in contact with LEU 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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27D LEU* 4.9 12.3 - - + -
30D SER* 4.7 13.5 - - - -
31D ARG* 4.9 9.0 - - - +
34D TYR* 3.5 41.9 + - + -
106F PHE* 4.0 12.1 - - + -
110F ILE* 3.8 35.2 - - + -
112F LEU* 5.2 4.0 - - + -
140F ALA 2.9 14.0 + - - +
141F LEU* 3.6 15.0 - - + +
143F LYS* 1.3 76.5 - - - +
145F TRP* 1.3 56.9 + - - +
147F SER* 3.3 8.9 + - - -
148F ALA* 2.8 27.9 + - - +
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Residues in contact with TRP 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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100F THR* 4.6 3.4 - - - -
101F ASN* 3.3 32.8 + - - +
102F VAL* 3.8 20.4 - - + -
103F PRO* 3.5 32.5 - - + -
105F TRP* 4.1 16.2 - + - -
106F PHE* 3.4 47.9 - + + -
141F LEU 2.9 18.3 + - - +
142F ALA 3.6 4.3 - - - +
143F LYS 3.2 0.2 - - - -
144F LEU* 1.3 74.7 - - - +
146F GLN* 1.3 74.9 + - - +
148F ALA* 2.9 14.8 + - + +
149F LEU* 2.9 52.2 + - + +
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Residues in contact with GLN 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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96F ILE* 3.6 27.6 - - + -
97F PRO* 4.1 21.8 - - - +
100F THR* 5.5 1.4 + - - -
101F ASN* 4.9 4.9 + - - -
142F ALA* 3.0 21.5 + - + +
143F LYS* 3.8 4.5 - - - +
145F TRP* 1.3 91.4 + - - +
147F SER* 1.3 61.4 + - - +
149F LEU* 3.3 24.6 + - - +
150F GLY* 3.4 14.2 + - - +
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Residues in contact with SER 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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23D PHE* 5.2 8.2 - - - +
34D TYR* 4.5 6.5 + - - -
143F LYS 3.0 14.2 + - - -
144F LEU* 3.4 14.1 - - - -
146F GLN* 1.3 75.9 - - - +
148F ALA* 1.3 64.7 + - - +
150F GLY* 3.0 15.3 + - - +
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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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23D PHE* 5.6 8.3 - - - +
106F PHE* 3.7 28.0 - - + -
144F LEU 2.8 14.0 + - - +
145F TRP* 2.9 13.9 + - + +
147F SER* 1.3 76.0 - - - +
149F LEU* 1.3 65.5 + - + +
150F GLY* 3.1 1.6 + - - -
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Residues in contact with LEU 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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101F ASN* 5.3 1.8 - - - +
145F TRP* 2.9 68.4 + - + +
146F GLN* 3.6 23.1 - - - +
147F SER 3.2 0.4 - - - -
148F ALA* 1.3 80.0 - - + +
150F GLY* 1.3 63.9 + - - +
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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