Contacts of the helix formed by residues 92 - 104 (chain A) in PDB entry 1AII
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.7 46.2 - - + +
51A ASN* 3.5 26.2 - - + +
90A THR 3.4 1.5 - - - +
91A PRO* 1.3 86.9 - - + +
93A ALA* 1.3 61.6 + - - +
95A PHE* 3.4 7.7 + - + +
96A ASP* 3.1 28.1 + - - +
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Residues in contact with ALA 93 (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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6A TRP* 3.7 26.9 - - + +
91A PRO* 3.4 2.3 - - + +
92A PRO* 1.3 79.8 - - - +
94A VAL* 1.3 65.9 + - + +
96A ASP* 3.5 2.9 + - - +
97A ALA* 3.1 23.0 + - - +
128A ASP* 4.1 31.2 - - + +
129A ILE* 4.2 5.1 - - - +
132A ALA* 4.1 9.3 - - + +
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Residues in contact with VAL 94 (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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70A LYS* 6.0 0.4 - - - +
90A THR* 3.8 8.5 - - + -
91A PRO* 3.1 27.9 + - + +
93A ALA* 1.3 77.8 - - + +
95A PHE* 1.3 57.5 + - - +
97A ALA* 3.2 7.8 + - + +
98A LYS* 2.9 57.5 + - + +
132A ALA* 4.1 16.4 - - + -
136A VAL* 4.7 17.0 - - + -
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Residues in contact with PHE 95 (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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87A ALA* 3.5 39.3 - - + -
90A THR* 3.5 19.0 - - + +
91A PRO 2.9 15.4 + - - +
92A PRO* 3.7 8.3 - - + +
93A ALA 3.4 0.2 - - - -
94A VAL* 1.3 76.1 - - - +
96A ASP* 1.3 66.6 + - - +
98A LYS* 3.2 7.2 + - + +
99A GLN* 2.8 68.1 + - + +
274A ASN* 4.5 3.4 - - + -
275A ARG* 4.0 33.7 - - + -
278A VAL* 4.1 17.9 - - + -
279A SER* 4.3 6.1 - - - -
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Residues in contact with ASP 96 (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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6A TRP* 3.4 13.4 - - - -
92A PRO 3.1 16.6 + - - +
93A ALA 4.0 0.2 - - - +
94A VAL 3.3 0.2 - - - -
95A PHE* 1.3 80.4 - - - +
97A ALA* 1.3 57.0 + - - +
99A GLN* 3.1 8.3 + - - +
100A LEU* 2.9 34.0 + - - +
117A ILE* 4.6 7.0 - - + +
121A ARG* 2.8 44.9 + - - -
129A ILE* 3.4 33.1 - - + +
275A ARG* 5.4 0.3 - - - +
279A SER* 4.1 9.1 - - - -
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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
----------------------------------------------------------
93A ALA 3.1 18.5 + - - +
94A VAL* 3.5 8.7 - - + +
96A ASP* 1.3 75.2 - - - +
98A LYS* 1.3 57.1 + - + +
100A LEU* 3.3 3.8 + - - +
101A LYS* 3.0 25.6 + - - +
129A ILE* 4.1 9.6 - - - +
132A ALA* 4.4 2.0 - - + -
133A TYR* 3.6 48.1 - - + +
136A VAL* 5.9 2.7 - - + -
137A TYR* 4.2 5.4 - - + -
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Residues in contact with LYS 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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70A LYS* 4.7 13.8 - - - +
90A THR* 4.3 14.4 - - + +
94A VAL* 2.9 42.2 + - + +
95A PHE* 3.7 8.1 - - + +
97A ALA* 1.3 75.6 - - + +
99A GLN* 1.3 63.2 + - - +
101A LYS* 3.4 2.3 + - - +
102A LYS* 2.9 31.1 + - - +
136A VAL* 4.2 18.9 - - + +
137A TYR* 3.3 20.4 + - + +
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Residues in contact with GLN 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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95A PHE* 2.8 58.4 + - + +
96A ASP* 3.5 6.5 - - - +
98A LYS* 1.3 80.9 - - - +
100A LEU* 1.3 59.2 + - - +
102A LYS* 3.3 39.6 + - - +
103A SER* 3.0 27.9 + - - -
113A ALA* 5.2 0.2 - - - +
117A ILE* 3.9 18.6 - - + +
271A PHE* 4.2 4.7 - - - +
275A ARG* 3.4 26.7 + - + +
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Residues in contact with LEU 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 ASP 2.9 14.6 + - - +
97A ALA* 3.6 6.3 - - - +
99A GLN* 1.3 73.0 - - - +
101A LYS* 1.3 64.8 + - - +
103A SER* 3.3 18.3 + - - -
104A MET* 3.4 17.1 - - + +
114A LEU* 3.8 24.0 - - + -
117A ILE* 3.9 36.1 - - + -
118A LEU* 4.3 16.4 - - + -
129A ILE* 3.5 31.9 - - + -
133A TYR* 4.2 6.7 - - + -
141A LEU* 3.6 28.7 - - + -
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Residues in contact with LYS 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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97A ALA 3.0 8.4 + - - +
98A LYS 3.8 1.1 - - - +
99A GLN 3.4 0.2 - - - -
100A LEU* 1.3 74.7 - - - +
102A LYS* 1.3 62.4 + - - +
104A MET* 3.2 15.8 + - + +
105A LYS* 3.4 47.9 + - + +
133A TYR* 3.2 24.6 - - - +
137A TYR* 3.4 58.7 - - + +
139A LYS* 4.3 25.1 - - - +
144A ASP* 4.6 2.0 - - - -
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Residues in contact with LYS 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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98A LYS 2.9 18.2 + - - +
99A GLN* 3.3 45.6 + - - +
101A LYS* 1.3 76.3 - - - +
103A SER* 1.3 67.8 + - - +
104A MET 3.3 0.9 + - - -
105A LYS* 3.5 20.5 + - - +
110A ASN* 5.7 4.0 - - - +
113A ALA* 5.1 0.8 - - - +
271A PHE* 3.5 40.7 - - + +
275A ARG* 3.6 14.8 - - - +
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Residues in contact with SER 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 GLN 3.0 15.8 + - - -
100A LEU* 3.4 14.6 - - - -
101A LYS 3.2 0.6 - - - -
102A LYS* 1.3 81.7 + - - +
104A MET* 1.3 55.7 + - - +
105A LYS 3.7 0.7 - - - -
109A THR* 3.5 5.9 - - - +
110A ASN* 2.6 50.7 + - - +
113A ALA* 3.0 27.4 - - - +
114A LEU* 4.2 11.2 - - - +
117A ILE* 5.2 0.3 - - - +
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Residues in contact with MET 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 LEU* 3.4 24.7 - - + +
101A LYS* 3.2 10.9 + - + +
103A SER* 1.3 79.9 - - - +
105A LYS* 1.3 54.4 + - - +
108A GLY 4.8 0.4 - - - -
109A THR* 4.7 4.3 - - + +
114A LEU* 3.8 25.6 - - + -
133A TYR* 4.0 9.9 - - - +
141A LEU* 4.0 15.7 - - + -
144A ASP* 3.6 33.4 - - + +
145A ILE* 3.7 28.0 - - + +
148A GLU* 3.7 26.1 - - + +
357A CA 2.8 20.3 - - - -
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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