Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 1POP
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 ASN 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 5.3 0.3 - - - +
114A GLN* 3.0 46.5 + - - +
115A PRO 3.3 3.8 - - - +
116A TYR* 1.3 79.4 - - - +
118A GLN* 1.3 63.4 + - - +
119A GLY* 3.0 17.8 + - - -
120A ALA* 3.0 21.3 + - - +
121A LEU* 3.5 12.1 + - - +
203A TYR* 4.2 6.9 - - - +
432A MOH 5.3 3.4 - - - +
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Residues in contact with GLN 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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116A TYR 4.2 0.2 - - - -
117A ASN* 1.3 73.1 + - - +
119A GLY* 1.3 61.2 + - - +
121A LEU* 3.3 5.1 + - - +
122A LEU* 3.1 33.4 + - + +
171A ILE* 5.2 0.7 - - + -
191A ARG* 2.9 31.8 + - + +
192A GLY* 3.0 32.9 + - - +
193A THR* 4.6 3.4 + - - +
194A GLY 5.5 1.8 - - - +
195A ASN 5.5 1.0 + - - -
203A TYR* 2.8 50.3 + - + +
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Residues in contact with GLY 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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1A ILE* 5.5 0.7 - - - +
117A ASN* 3.0 8.0 + - - -
118A GLN* 1.3 75.1 - - - +
120A ALA* 1.3 65.5 + - - +
122A LEU* 3.4 11.3 + - - +
123A TYR* 3.0 25.6 + - - +
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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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113A VAL* 4.4 7.2 - - + -
114A GLN* 4.0 25.4 - - + +
117A ASN* 3.0 31.6 + - - +
118A GLN 3.3 0.2 - - - -
119A GLY* 1.3 77.6 - - - +
121A LEU* 1.3 55.4 + - - +
123A TYR* 3.4 7.0 + - - +
124A SER* 3.0 32.6 + - - -
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Residues in contact with LEU 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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113A VAL* 4.3 12.3 - - + +
117A ASN 3.5 8.1 + - - +
118A GLN* 3.3 9.8 + - - +
119A GLY 3.3 0.4 - - - -
120A ALA* 1.3 76.4 - - - +
122A LEU* 1.3 59.6 + - + +
124A SER* 3.2 4.3 + - - +
125A ILE* 2.9 46.0 + - + +
130A VAL* 4.1 11.9 - - + -
132A VAL* 4.1 19.5 - - + -
171A ILE* 4.1 13.9 - - + -
202A LEU* 4.5 6.7 - - + +
203A TYR* 3.6 34.8 - - + -
206A SER* 3.8 28.7 - - - +
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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
----------------------------------------------------------
1A ILE* 4.2 11.4 - - + -
118A GLN* 3.1 30.2 + - + +
119A GLY* 3.4 8.0 + - - +
121A LEU* 1.3 76.1 - - + +
123A TYR* 1.3 61.7 + - - +
125A ILE* 3.4 2.5 + - + -
126A ALA* 3.0 21.1 + - - +
166A TYR* 3.5 51.2 - - + -
171A ILE* 4.4 12.1 - - + -
191A ARG* 3.4 42.6 - - - +
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Residues in contact with TYR 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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1A ILE* 3.9 34.2 - - + +
119A GLY 3.0 18.3 + - - +
120A ALA* 3.7 7.2 - - - +
122A LEU* 1.3 75.0 - - - +
124A SER* 1.3 66.7 + - - +
126A ALA* 3.5 7.9 + - - +
127A ASN* 3.6 29.1 + - - +
412A MOH 4.9 8.3 - - - -
415A MOH 5.8 2.2 - - - -
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Residues in contact with SER 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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113A VAL* 3.9 21.9 - - - +
120A ALA 3.0 15.0 + - - -
121A LEU* 3.2 6.7 + - - -
123A TYR* 1.3 78.8 - - - +
125A ILE* 1.3 56.8 + - - +
127A ASN* 2.8 21.5 + - - +
128A GLN* 3.1 13.7 + - - +
130A VAL* 3.9 17.9 - - - -
208A TYR* 4.3 5.4 + - - -
415A MOH 3.4 21.9 + - - -
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Residues in contact with ILE 125 (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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5A VAL* 4.0 1.7 - - + +
7A TRP* 2.8 28.7 + - - +
121A LEU* 2.9 40.0 + - + +
122A LEU* 3.9 7.2 - - + +
124A SER* 1.3 73.8 - - - +
126A ALA* 1.3 59.3 + - - +
127A ASN 3.1 0.7 + - - -
128A GLN 3.3 11.5 - - - +
130A VAL* 4.6 9.4 - - + -
163A ALA* 3.6 31.0 - - + +
164A VAL 4.3 2.7 - - - -
165A GLY* 3.6 40.2 - - - +
166A TYR* 3.9 9.9 - - + -
171A ILE* 4.2 17.5 - - + -
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Residues in contact with ALA 126 (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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1A ILE* 3.9 22.0 - - + -
2A PRO* 4.6 3.7 - - + +
5A VAL* 4.2 18.4 - - + +
7A TRP* 3.7 10.9 - - - -
122A LEU 3.0 16.7 + - - +
123A TYR 3.8 6.1 - - - +
124A SER 3.2 0.2 - - - -
125A ILE* 1.3 75.8 - - - +
127A ASN* 1.3 60.0 + - - +
166A TYR* 3.9 19.0 - - + +
412A MOH 3.8 11.2 + - - +
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Residues in contact with ASN 127 (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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7A TRP* 3.5 13.6 - - - -
40A ILE* 3.7 6.6 - - - +
123A TYR* 3.6 29.8 + - - +
124A SER 2.8 11.0 + - - +
126A ALA* 1.3 78.1 - - - +
128A GLN* 1.3 59.8 + - - +
412A MOH 2.6 35.6 + - - -
415A MOH 3.5 30.6 + - - +
431A MOH 3.6 30.0 - - - +
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Residues in contact with GLN 128 (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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7A TRP* 3.7 11.7 - - - +
33A THR 5.5 0.6 + - - +
37A ILE* 3.7 21.3 - - + +
40A ILE* 4.0 9.2 - - + -
124A SER 3.1 17.8 + - - +
125A ILE* 3.3 14.6 + - - +
127A ASN* 1.3 77.0 - - - +
129A PRO* 1.3 78.3 + - + +
130A VAL* 3.6 3.1 - - + +
208A TYR* 3.4 25.6 - - + +
209A PRO* 2.9 34.3 + - - +
415A MOH 3.3 26.8 - - - +
431A MOH 3.6 9.2 + - - -
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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