Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 1P7X
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 HIS 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.4 23.0 - - + +
90A GLN* 2.6 34.1 + - - +
91A TYR* 2.9 8.0 + - - +
93A GLN* 1.3 75.0 - - - +
95A SER* 1.3 51.6 + - - +
96A GLN* 2.7 35.2 + - + +
97A ALA* 2.8 40.5 + - + +
98A LEU* 2.9 13.7 - - + +
101A PHE* 3.4 19.1 - + - -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 4.1 1.3 - - - -
61A ASP* 2.9 29.2 - - - +
63A GLY* 3.4 23.9 + - - -
78A ALA* 4.4 14.2 - - - +
79A PRO 4.8 0.9 + - - -
80A PHE* 4.3 6.8 - - - +
91A TYR 2.7 13.0 + - - -
92A GLN* 2.7 24.9 + - - -
93A GLN 3.4 0.4 - - - -
94A HIS* 1.3 72.4 - - - +
96A GLN* 1.3 61.1 + - - +
98A LEU* 3.2 23.7 - - - +
99A GLY 3.4 1.2 + - - -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 2.6 58.2 + - + +
93A GLN* 2.8 36.4 + - - +
94A HIS* 2.7 25.0 + - + +
95A SER* 1.3 74.4 + - - +
97A ALA* 1.3 60.2 + - - +
99A GLY* 3.3 4.9 + - - -
100A LYS* 2.6 40.5 + - + +
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Residues in contact with ALA 97 (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 HIS* 2.8 44.8 + - + +
96A GLN* 1.3 83.8 - - + +
98A LEU* 1.3 55.9 + - - +
100A LYS* 3.4 14.6 - - + -
101A PHE* 2.4 53.5 + - + -
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Residues in contact with LEU 98 (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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62A GLY 4.2 1.1 - - - +
80A PHE* 3.0 59.7 - - + -
81A ASP 3.4 2.2 - - - +
82A VAL* 3.1 38.6 - - + +
86A LEU* 5.0 9.0 - - + -
91A TYR* 3.7 12.1 - - - +
94A HIS* 2.9 41.7 - - + +
95A SER 3.2 9.0 - - - +
97A ALA* 1.3 74.9 - - + +
99A GLY* 1.3 54.1 + - - +
101A PHE* 4.2 1.6 - - + -
102A LEU* 2.8 36.5 + - - +
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Residues in contact with GLY 99 (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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62A GLY* 3.0 33.4 + - - -
95A SER 3.4 0.4 + - - -
96A GLN 3.3 6.0 + - - -
97A ALA 3.1 0.4 - - - -
98A LEU* 1.3 77.8 - - - +
100A LYS* 1.3 48.4 + - - +
102A LEU* 3.2 5.3 + - - +
103A GLN* 2.5 44.1 + - - +
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Residues in contact with LYS 100 (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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96A GLN* 2.6 25.5 + - + +
97A ALA* 2.8 15.3 + - + +
99A GLY* 1.3 67.5 - - - -
101A PHE* 1.3 57.3 + - + +
103A GLN* 4.2 4.9 - - - -
104A ASP* 2.6 67.3 + - - +
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Residues in contact with PHE 101 (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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84A ILE* 3.1 38.1 - - + -
86A LEU* 3.8 15.3 - - + -
94A HIS* 3.4 17.7 - + - -
97A ALA* 2.4 59.1 + - + +
98A LEU* 3.8 2.7 - - - +
100A LYS* 1.3 67.1 - - + +
102A LEU* 1.3 56.5 - - - +
104A ASP* 4.9 1.1 - - - -
105A ILE* 2.8 46.1 + - + +
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Residues in contact with LEU 102 (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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81A ASP* 3.4 15.9 - - + +
82A VAL* 3.3 33.2 - - + +
83A GLY* 3.3 17.7 - - - +
98A LEU 2.8 17.6 + - - +
99A GLY* 3.7 4.0 - - - +
101A PHE* 1.3 73.9 - - - +
103A GLN* 1.3 52.1 + - - +
105A ILE* 2.8 36.2 - - + +
106A LEU 4.9 0.2 - - - -
107A TRP* 5.8 0.2 - - - -
110A ALA* 3.4 35.5 - - + +
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Residues in contact with GLN 103 (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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99A GLY* 2.5 25.7 + - - +
100A LYS* 4.1 3.6 - - - +
102A LEU* 1.3 70.8 - - - +
104A ASP* 1.3 80.6 + - - +
105A ILE 3.2 8.0 - - - +
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Residues in contact with ASP 104 (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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100A LYS* 2.6 67.1 + - - +
101A PHE* 4.3 1.8 - - - +
103A GLN* 1.3 83.6 - - - +
105A ILE* 1.3 61.7 + - + +
106A LEU* 3.9 1.0 + - - +
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Residues in contact with ILE 105 (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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84A ILE* 4.7 17.9 - - + -
101A PHE* 2.8 41.2 + - + +
102A LEU* 2.8 41.9 - - + +
103A GLN 3.2 8.7 - - - +
104A ASP* 1.3 79.7 - - + +
106A LEU* 1.3 62.3 + - - +
107A TRP 3.9 0.3 + - - -
109A GLU* 4.4 10.1 - - + +
110A ALA* 3.2 35.9 - - - +
113A ALA* 5.3 0.4 - - + -
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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