Contacts of the helix formed by residues 112 - 123 (chain A) in PDB entry 1PVS
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 ASP 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.8 2.5 - - + -
77A LYS* 4.4 10.9 + - - +
110A CYS* 3.6 8.6 - - - +
111A VAL* 1.3 84.9 - - + +
113A ALA* 1.3 63.8 + - - +
114A PHE* 3.4 15.7 - - - +
115A GLU* 3.2 33.4 + - + +
116A GLN 3.1 18.5 + - - -
196A MET* 3.4 19.6 - - - +
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Residues in contact with ALA 113 (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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110A CYS* 4.0 10.7 - - - -
112A ASP* 1.3 75.1 + - - +
114A PHE* 1.3 57.8 + - - +
116A GLN* 3.9 1.9 - - - -
117A GLY* 2.9 24.6 + - - -
194A LEU* 4.6 2.1 - - + +
195A PRO 4.0 6.5 - - - +
196A MET* 3.5 45.2 + - + +
223A PHE* 3.7 16.6 - - + -
227A GLY 4.1 11.9 - - - +
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Residues in contact with PHE 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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112A ASP* 3.3 13.2 - - - +
113A ALA* 1.3 75.6 - - - +
115A GLU* 1.3 68.1 + - - +
117A GLY* 3.5 1.0 + - - -
118A VAL* 3.0 51.7 + - + +
155A PHE* 4.6 2.7 - + - -
156A PRO 3.5 24.5 - - - -
158A PRO* 3.6 36.6 - - + -
161A LEU* 3.7 17.7 - - + -
182A LEU 5.2 0.4 - - - -
185A LEU* 4.0 14.5 - - + +
186A ALA* 3.8 22.9 - - + -
189A ALA* 3.8 21.8 - - + -
194A LEU* 4.2 9.2 - - + -
196A MET* 3.4 15.6 - - + +
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Residues in contact with GLU 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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37A ARG* 2.6 36.8 + - - -
110A CYS* 6.3 0.7 - - - -
111A VAL* 5.0 3.5 - - - +
112A ASP* 3.2 27.1 + - + +
114A PHE* 1.3 77.2 - - - +
116A GLN* 1.3 64.8 + - - +
118A VAL* 2.8 21.8 + - - +
119A ARG* 2.7 49.1 + - - +
155A PHE* 3.3 50.4 - - + +
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Residues in contact with GLN 116 (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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109A GLY 4.1 0.4 + - - -
110A CYS* 3.2 29.4 - - + +
112A ASP 3.1 12.0 + - - +
113A ALA 3.9 3.8 - - - +
115A GLU* 1.3 82.1 + - - +
117A GLY* 1.3 64.6 + - - +
119A ARG* 2.9 32.3 + - - +
120A ALA* 2.8 24.2 + - + +
222A TYR* 4.7 7.0 - - + -
223A PHE* 4.6 5.4 - - + +
226A ARG* 3.2 55.8 + - + +
227A GLY* 3.8 13.9 - - - +
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Residues in contact with GLY 117 (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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113A ALA 2.9 17.9 + - - -
114A PHE* 3.9 2.2 - - - -
116A GLN* 1.3 75.7 - - - +
118A VAL* 1.3 62.7 + - - +
120A ALA* 3.3 4.4 + - - +
121A ILE* 3.2 27.5 + - - +
185A LEU* 3.7 16.8 - - - -
194A LEU* 5.8 0.2 - - - -
219A THR* 5.2 0.2 - - - +
223A PHE* 3.7 20.8 - - - -
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Residues in contact with VAL 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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114A PHE* 3.0 44.8 + - + +
115A GLU 2.8 10.2 + - - +
117A GLY* 1.3 77.3 - - - +
119A ARG* 1.3 59.2 + - - +
121A ILE* 3.5 3.1 + - - +
122A LEU* 3.1 37.0 + - + +
138A VAL* 5.4 4.5 - - + -
155A PHE* 3.4 27.8 - - + -
161A LEU* 4.4 11.2 - - + -
182A LEU* 4.1 18.3 - - + +
185A LEU* 3.6 9.6 - - + -
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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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22A ARG* 3.2 25.5 + - - +
24A VAL* 3.9 16.2 - - - +
27A VAL* 5.0 2.2 - - - +
28A GLU* 2.6 39.9 + - - +
37A ARG* 3.7 7.5 - - - +
115A GLU* 2.7 50.3 + - + +
116A GLN* 2.9 32.6 + - - +
118A VAL* 1.3 75.0 - - - +
120A ALA* 1.3 54.9 + - - +
122A LEU* 3.1 8.7 + - - +
123A GLY* 2.7 33.6 + - - -
131A ALA* 5.6 0.9 - - - +
135A THR* 4.8 11.0 - - + +
155A PHE* 4.6 9.3 - - + -
222A TYR* 5.7 2.6 - - + -
226A ARG* 5.8 3.9 - - - +
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Residues in contact with ALA 120 (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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116A GLN* 2.8 15.8 + - + +
117A GLY 3.6 8.1 - - - +
119A ARG* 1.3 71.7 - - - +
121A ILE* 1.3 64.5 + - - +
123A GLY* 3.0 11.7 + - - -
124A GLN* 3.4 8.1 + - - +
218A TRP* 3.6 10.6 - - - -
219A THR* 3.9 27.3 - - + +
222A TYR* 4.1 29.1 - - + -
223A PHE* 4.3 12.3 - - + +
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Residues in contact with ILE 121 (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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117A GLY 3.2 14.2 + - - +
118A VAL 3.7 1.3 - - - +
120A ALA* 1.3 75.3 - - - +
122A LEU* 1.3 57.7 + - - +
124A GLN* 3.0 52.4 + - - +
178A ARG* 3.5 22.7 - - + +
181A ALA* 4.1 24.7 - - + +
182A LEU* 3.5 34.1 - - + -
185A LEU* 4.1 17.3 - - + -
215A ILE* 4.6 14.1 - - + -
219A THR* 4.1 15.0 - - + -
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Residues in contact with LEU 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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118A VAL* 3.1 38.3 + - + +
119A ARG 3.6 4.3 - - - +
121A ILE* 1.3 75.7 - - - +
123A GLY* 1.3 58.5 + - - +
124A GLN 3.2 5.3 + - - +
126A VAL* 4.3 5.2 - - - +
131A ALA* 3.9 16.3 - - + +
134A LEU* 3.7 21.6 - - + +
135A THR* 3.2 44.0 - - + +
138A VAL* 4.2 13.0 - - + -
174A MET* 3.5 33.4 - - + -
178A ARG* 4.7 5.9 + - + +
182A LEU* 4.0 12.8 - - + -
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Residues in contact with GLY 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 2.7 13.0 + - - -
120A ALA* 3.0 8.4 + - - -
122A LEU* 1.3 77.2 - - - +
124A GLN* 1.3 56.1 + - - +
126A VAL 3.4 7.6 - - - +
131A ALA* 4.1 15.9 - - - -
218A TRP* 3.7 10.1 - - - -
222A TYR* 6.3 1.1 - - - -
800A 7HP 2.7 31.9 + - - -
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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