Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 1PV2
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A PHE* 1.3 64.2 + - + +
120A PHE* 3.3 11.4 + - + +
121A GLU* 3.1 41.2 - - + +
122A GLN* 2.5 32.6 + - - +
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Residues in contact with PHE 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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79A LEU* 4.2 31.0 - - + -
82A LEU* 4.1 9.4 - - + -
83A TYR* 3.5 57.9 - + + -
86A HIS* 4.4 10.3 - - + -
92A PHE* 4.7 11.9 - + - -
118A PRO* 1.3 82.1 - - + +
120A PHE* 1.3 69.5 + - - +
122A GLN* 3.3 16.0 + - + +
123A HIS* 3.3 51.5 + + + +
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Residues in contact with PHE 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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75A PRO* 6.4 1.8 - - + -
79A LEU* 4.1 33.7 - - + +
104A PHE* 3.9 25.8 - + - -
106A TYR* 3.7 39.3 - + - -
118A PRO* 4.1 10.9 - - + +
119A PHE* 1.3 80.2 - - - +
121A GLU* 1.3 61.8 + - - +
123A HIS* 2.8 6.5 + - + -
124A LYS* 2.7 68.7 + - + -
127A PHE* 4.1 11.7 - + + -
16B ASP* 4.3 7.2 - - - -
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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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118A PRO* 3.1 38.5 - - + +
120A PHE* 1.3 80.3 - - - +
122A GLN* 1.3 63.2 + - + +
123A HIS 3.2 0.9 + - - -
124A LYS* 3.4 41.6 + - - +
125A SER 4.7 0.7 + - - -
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Residues in contact with GLN 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 PRO* 2.5 30.3 + - - +
119A PHE* 3.3 13.9 + - - +
120A PHE 3.0 1.0 + - - -
121A GLU* 1.3 80.6 - - + +
123A HIS* 1.3 72.9 + - + +
125A SER* 5.2 2.4 + - - -
86H HIS* 4.3 20.3 - - + -
122H GLN* 4.4 17.4 + - - +
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Residues in contact with HIS 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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79A LEU* 6.4 0.4 - - + -
86A HIS* 5.9 2.4 - - + +
91A GLU* 4.5 20.5 + - - -
92A PHE* 3.9 26.4 - + + -
119A PHE* 3.3 48.2 + + + +
120A PHE* 2.8 6.4 + - + +
122A GLN* 1.3 87.1 - - + +
124A LYS* 1.3 67.2 + - - +
125A SER* 3.0 5.2 - - - -
126A LEU* 2.8 41.7 + - + +
127A PHE* 3.8 7.8 + - + -
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Residues in contact with LYS 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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106A TYR* 5.7 0.7 - - - +
120A PHE* 2.7 57.0 + - + +
121A GLU* 3.4 35.2 + - - +
123A HIS* 1.3 71.8 - - - +
125A SER* 1.3 62.4 + - - +
126A LEU 3.0 0.7 + - - -
127A PHE* 3.1 7.0 + - + +
128A ARG* 3.0 53.2 + - + +
16B ASP* 3.1 25.7 + - - +
17B ASN* 5.5 5.9 - - - +
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Residues in contact with SER 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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121A GLU 4.7 1.4 + - - -
122A GLN 5.6 2.2 - - - -
123A HIS* 2.8 6.0 + - - -
124A LYS* 1.3 75.8 - - - +
126A LEU* 1.3 65.6 + - - +
128A ARG* 4.0 3.6 - - - +
129A ASN* 3.2 39.3 + - - +
42H PRO 5.2 5.6 - - - -
43H LYS* 5.6 5.7 + - - -
44H PRO* 4.4 24.2 - - - +
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Residues in contact with LEU 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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91A GLU* 5.9 1.8 - - + +
92A PHE* 3.8 38.6 - - + +
93A GLU* 4.6 10.5 - - + -
94A VAL* 3.5 18.2 - - + +
123A HIS* 2.8 38.5 + - + +
125A SER* 1.3 79.7 + - - +
127A PHE* 1.3 61.3 + - - +
128A ARG 3.7 0.2 + - - -
129A ASN 3.7 4.8 - - - +
130A PRO* 3.7 14.7 - - - +
46H ARG* 3.7 44.9 - - - +
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Residues in contact with PHE 127 (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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53A VAL* 4.6 9.2 - - + -
55A ALA* 5.1 1.8 - - + -
78A THR* 3.5 22.0 - - - -
79A LEU* 3.9 21.1 - - + -
82A LEU* 3.9 16.8 - - + -
92A PHE* 3.8 18.4 - + - -
94A VAL* 3.5 23.6 - - + -
102A THR* 2.7 47.0 + - + +
104A PHE* 3.6 33.2 - + + -
120A PHE* 4.1 13.5 - + + -
123A HIS* 4.3 12.1 - - + -
124A LYS* 3.1 8.0 + - + +
126A LEU* 1.3 77.9 - - - +
128A ARG* 1.3 60.9 + - - +
130A PRO* 3.5 6.4 - - - +
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Residues in contact with ARG 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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101A MET* 3.3 42.8 - - - +
102A THR 5.8 0.2 - - - -
124A LYS* 3.0 55.0 + - + +
125A SER* 4.3 1.7 - - - +
127A PHE* 1.3 77.6 - - - +
129A ASN* 1.3 77.5 + - - +
130A PRO* 3.3 3.4 - - - +
15B GLU* 6.0 0.2 - - - -
16B ASP* 3.6 22.9 + - - +
17B ASN* 4.7 5.5 - - - +
62B PRO* 5.7 4.9 - - - +
66B GLY* 3.2 25.7 + - - -
68B LEU* 3.9 27.5 - - - +
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Residues in contact with ASN 129 (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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125A SER* 3.2 27.4 + - - +
126A LEU* 3.7 8.5 - - - +
128A ARG* 1.3 95.1 + - - +
130A PRO* 1.3 65.9 - - - +
131A LYS* 5.4 0.9 - - - +
43H LYS* 4.6 19.4 + - - +
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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