Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 3PMM
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.8 21.8 - - + +
64A GLU 4.3 4.0 - - - +
68A GLY* 3.8 23.6 - - - +
71A LEU* 4.1 5.4 - - + -
93A TRP* 3.9 31.2 - - + -
94A PHE* 3.4 14.7 - - + -
108A ASN 4.2 1.6 - - - +
109A THR 3.2 15.3 - - - +
110A MSE 3.4 0.9 - - - -
111A ALA* 1.3 94.3 - - + +
113A PHE* 1.3 65.4 + - + +
114A LEU 3.1 0.4 - - - -
115A THR* 3.2 7.5 + - - +
116A LEU 3.1 15.6 + - - -
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Residues in contact with PHE 113 (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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63A TRP* 3.7 25.1 - + - -
94A PHE* 5.6 1.3 - + - -
98A PHE* 4.3 6.1 - + - -
109A THR 3.8 2.2 - - - -
110A MSE 3.0 26.0 + - - +
112A PRO* 1.3 76.8 - - + +
114A LEU* 1.3 64.6 + - - +
116A LEU* 3.7 24.1 - - + +
117A ALA* 3.0 23.7 + - - +
131A TRP* 3.9 33.7 - + + -
132A LEU* 3.9 9.3 - - + +
135A TRP* 3.2 59.5 - + + -
175A PRO* 4.5 4.9 - - + -
179A ILE* 4.4 17.2 - - + +
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Residues in contact with LEU 114 (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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72A TYR* 3.5 43.7 - - + +
111A ALA 3.3 12.2 + - - +
113A PHE* 1.3 81.2 - - - +
115A THR* 1.3 62.5 + - - +
117A ALA* 3.3 10.6 + - - +
118A TYR* 3.2 31.7 + - + +
174A LEU* 3.7 35.4 - - + +
175A PRO* 3.9 17.2 - - + +
178A LYS* 3.6 29.6 - - + -
388A FMT 3.9 14.6 - - - +
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Residues in contact with THR 115 (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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68A GLY 4.4 1.9 + - - -
71A LEU* 3.5 14.1 - - + +
72A TYR* 3.2 36.2 + - - +
75A TYR* 3.9 22.1 - - + +
90A ILE* 3.9 28.3 - - + -
94A PHE* 4.0 4.9 - - + -
111A ALA 4.5 0.2 + - - -
112A PRO* 3.2 9.1 + - - +
114A LEU* 1.3 75.8 - - - +
116A LEU* 1.3 67.1 + - - +
118A TYR* 3.2 10.0 + - - +
119A ARG* 3.0 22.1 + - + +
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Residues in contact with LEU 116 (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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94A PHE* 3.7 39.8 - - + -
98A PHE* 3.9 13.0 - - + -
112A PRO 3.1 8.4 + - - +
113A PHE* 3.7 37.7 - - + +
114A LEU 3.3 0.2 - - - -
115A THR* 1.3 77.4 - - - +
117A ALA* 1.3 56.9 + - - +
119A ARG* 3.2 3.3 + - + +
120A PHE* 2.8 28.4 + - - +
128A TYR* 3.7 44.6 - - + +
131A TRP* 4.0 11.2 - - + -
132A LEU* 3.8 14.1 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE 3.0 18.0 + - - +
114A LEU* 3.5 6.7 - - - +
115A THR 3.2 0.2 - - - -
116A LEU* 1.3 77.0 - - - +
118A TYR* 1.3 56.9 + - - +
120A PHE* 3.3 0.7 + - - +
121A GLU* 2.9 25.2 + - - +
132A LEU* 3.8 16.5 - - + +
178A LYS* 3.7 23.3 - - + -
179A ILE* 4.2 10.8 - - + +
182A LEU* 3.2 24.7 - - + +
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Residues in contact with TYR 118 (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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72A TYR* 4.3 12.9 + + - -
75A TYR* 3.4 40.5 + + + -
79A GLN* 4.3 3.6 - - - -
114A LEU* 3.2 46.6 + - + +
115A THR* 3.2 9.7 + - - +
117A ALA* 1.3 78.6 - - - +
119A ARG* 1.3 62.1 + - - +
121A GLU* 3.3 18.5 + - - +
122A GLU* 3.1 28.9 + - - +
178A LYS* 3.5 28.7 + - - +
244A GLU* 5.4 0.5 + - - -
245A LEU* 4.9 7.3 - - - +
382A FMT 3.5 32.2 + - - -
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Residues in contact with ARG 119 (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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75A TYR* 4.2 13.0 - - + -
78A TYR* 3.8 11.9 + - - -
87A ARG* 3.6 20.6 - - - +
90A ILE* 4.0 24.9 - - + +
91A ASP* 2.9 39.9 + - - +
94A PHE* 5.0 1.8 - - + -
115A THR* 3.0 19.0 + - + +
116A LEU* 3.7 8.1 - - + +
118A TYR* 1.3 73.4 - - - +
120A PHE* 1.3 61.0 + - - +
122A GLU* 2.9 39.1 + - - +
123A THR* 2.8 67.9 + - - +
125A ARG* 3.7 4.8 - - - +
128A TYR* 4.1 15.7 - - + +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU 2.8 16.7 + - - +
117A ALA 3.6 3.6 - - - +
119A ARG* 1.3 75.8 - - - +
121A GLU* 1.3 59.4 + - - +
123A THR* 4.0 1.6 - - - -
124A GLY* 2.8 34.8 + - - -
125A ARG 3.3 30.3 - - - -
128A TYR* 3.8 18.0 - - + -
129A LEU* 4.0 32.3 - - + -
132A LEU* 3.8 17.9 - - + -
182A LEU* 3.7 21.8 - - + -
183A LEU* 4.3 8.7 - - + -
385A FMT 3.7 28.5 - - - -
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Residues in contact with GLU 121 (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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117A ALA 2.9 12.8 + - - +
118A TYR* 3.4 20.4 - - - +
120A PHE* 1.3 79.8 - - - +
122A GLU* 1.3 63.3 + - + +
124A GLY 4.6 0.9 + - - -
178A LYS* 2.8 31.7 + - - -
182A LEU* 3.8 25.1 - - + +
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Residues in contact with GLU 122 (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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75A TYR* 3.2 33.1 - - - +
78A TYR* 3.2 28.8 + - - -
118A TYR 3.1 13.6 + - - +
119A ARG* 2.9 29.8 + - - +
121A GLU* 1.3 80.9 - - + +
123A THR* 1.3 60.9 + - + +
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Residues in contact with THR 123 (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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119A ARG* 2.8 62.5 + - - +
120A PHE* 4.0 1.0 - - - -
122A GLU* 1.3 76.3 - - + +
124A GLY* 1.3 65.4 + - - +
125A ARG* 3.1 46.2 + - - +
128A TYR* 4.1 1.0 - - - -
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Residues in contact with GLY 124 (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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120A PHE* 2.8 34.4 + - - -
121A GLU 4.6 1.0 + - - -
122A GLU 3.7 0.6 - - - -
123A THR* 1.3 72.0 + - - +
125A ARG* 1.3 61.5 + - - +
126A MSE 3.0 1.6 + - - +
385A FMT 2.8 25.6 - - - +
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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