Contacts of the helix formed by residues 92 - 103 (chain A) in PDB entry 4AUP
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 SER 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PRO* 1.3 77.2 - - - +
94A VAL* 3.3 23.1 - - - +
95A SER* 3.3 20.6 + - - -
96A ASP* 3.1 35.8 + - - +
120A ASN* 5.4 0.4 - - - -
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Residues in contact with PRO 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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92A SER* 1.3 86.4 - - - +
94A VAL* 1.3 57.1 + - + +
96A ASP* 4.9 0.2 - - + -
97A THR* 2.7 37.2 + - - -
120A ASN* 4.3 21.5 - - + +
121A LEU* 3.7 8.1 - - + +
157A GLN* 3.6 17.9 + - + +
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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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92A SER* 3.5 12.1 - - - +
93A PRO* 1.3 80.1 - - + +
95A SER* 1.3 61.5 + - - +
96A ASP 3.3 0.2 - - - -
97A THR 3.4 0.3 + - - -
98A ASP* 3.1 35.0 + - - +
157A GLN* 3.7 16.2 - - + +
158A HIS* 4.2 19.3 - - + +
159A ARG* 3.5 35.9 + - - +
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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
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92A SER* 3.3 26.8 + - - -
94A VAL* 1.3 80.9 - - - +
96A ASP* 1.3 64.7 + - - +
98A ASP* 4.0 4.4 - - - +
99A ARG* 3.0 28.6 + - - +
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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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92A SER 3.1 26.6 + - - +
93A PRO* 4.1 3.3 - - - +
95A SER* 1.3 86.7 + - - +
97A THR* 1.3 64.3 + - - +
99A ARG* 3.9 23.8 + - - +
100A LEU* 3.1 30.7 + - - +
118A PRO* 3.9 31.2 - - + +
120A ASN* 5.0 2.3 + - - +
121A LEU* 4.6 4.0 - - + -
99B ARG* 5.2 3.8 - - - -
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Residues in contact with THR 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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93A PRO 2.7 23.9 + - - -
94A VAL 3.8 0.2 - - - -
95A SER 3.4 0.2 - - - -
96A ASP* 1.3 75.8 - - - +
98A ASP* 1.3 58.4 + - - +
100A LEU 3.4 0.9 + - - -
101A LEU* 2.9 32.4 + - + +
121A LEU* 3.4 11.5 - - - +
149A PHE* 3.6 26.4 - - + +
153A ASN* 4.1 11.9 - - + +
154A TYR* 3.8 16.6 - - + -
157A GLN* 2.9 16.8 + - - +
159A ARG* 3.7 23.3 - - - +
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Residues in contact with ASP 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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94A VAL* 3.1 17.4 + - - +
95A SER* 4.2 5.0 - - - +
97A THR* 1.3 73.9 - - - +
99A ARG* 1.3 58.9 + - - +
101A LEU* 4.2 0.4 - - - -
102A TYR* 2.9 50.1 + - + +
103A SER* 3.9 1.4 + - - -
154A TYR* 2.7 29.1 + - - -
159A ARG* 3.0 26.4 + - - -
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Residues in contact with ARG 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 SER 3.0 19.7 + - - +
96A ASP* 3.9 21.6 + - - +
98A ASP* 1.3 76.0 - - - +
100A LEU* 1.3 91.2 + - - +
103A SER* 3.1 34.4 + - - +
104A THR* 2.7 31.5 + - - +
117A ASN 5.3 1.4 + - - -
118A PRO* 4.9 5.9 - - - +
96B ASP* 5.4 4.7 - - - -
99B ARG* 3.3 58.4 - - - +
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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 3.1 22.3 + - - +
97A THR 3.8 3.4 - - - +
99A ARG* 1.3 105.0 - - - +
101A LEU* 1.3 53.6 + - - +
104A THR* 3.5 17.8 - - + +
108A ALA 5.0 0.2 - - - +
109A PHE* 3.6 21.2 - - + -
112A ALA* 3.7 25.8 - - + -
117A ASN 4.2 0.7 - - - +
118A PRO* 4.0 18.8 - - + -
121A LEU* 4.7 0.9 - - + -
123A TRP* 3.8 25.1 - - + -
146A ARG* 2.8 30.5 + - - -
149A PHE* 4.0 15.0 - - + -
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Residues in contact with LEU 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 THR* 2.9 21.9 + - + +
98A ASP 3.8 3.1 - - - +
100A LEU* 1.3 77.1 - - - +
102A TYR* 1.3 88.1 + - + +
103A SER 3.8 0.2 - - - -
146A ARG* 3.5 53.6 + - + +
149A PHE* 4.1 6.4 - - + -
150A GLY* 3.8 20.9 - - - +
154A TYR* 3.5 31.0 - - + -
168A ILE* 4.4 9.9 - - + -
171A ASN* 3.0 27.5 + - - +
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Residues in contact with TYR 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 ASP* 2.9 40.7 + - + +
101A LEU* 1.3 87.5 - - + +
103A SER* 1.3 66.0 + - - +
104A THR 3.8 1.8 - - - -
154A TYR* 3.1 28.2 + - - -
167A ARG* 3.6 38.2 - - + +
168A ILE* 3.5 21.1 - - - +
171A ASN* 3.8 36.0 + - + +
174A LYS* 4.4 15.9 + - - -
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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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98A ASP 3.9 0.5 + - - -
99A ARG* 3.1 22.9 + - - +
102A TYR* 1.3 83.6 + - - +
104A THR* 1.3 64.6 + - - +
117B ASN* 2.9 26.2 + - - +
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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