Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 1ASC
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY 3.6 9.2 - - - +
83A ILE* 1.3 85.5 - - + +
85A GLU* 1.3 63.7 + - + +
87A GLY* 3.2 10.2 + - - -
88A ARG* 3.2 38.1 + - + +
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Residues in contact with GLU 85 (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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83A ILE* 3.5 7.5 - - + +
84A PRO* 1.3 77.7 - - - +
86A PHE* 1.3 63.3 + - - +
88A ARG* 3.2 34.7 + - - +
89A CYS* 2.9 33.8 + - - -
307A ALA* 4.1 14.8 - - + -
311A SER* 3.6 32.3 + - - -
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Residues in contact with PHE 86 (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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83A ILE* 3.2 26.0 + - + +
85A GLU* 1.3 78.7 - - - +
87A GLY* 1.3 56.3 - - - +
89A CYS* 3.3 5.7 + - - +
90A THR* 2.6 45.3 + - - -
109A THR* 4.9 0.2 - - + -
111A GLN* 3.8 24.9 - - + -
256A TYR* 3.2 42.4 - + - -
267A VAL* 3.8 16.6 - - + -
268A GLY 3.7 23.3 - - - -
269A ALA* 4.1 7.0 - - + -
303A ALA* 3.6 23.3 - - + +
306A VAL* 4.0 12.3 - - + -
307A ALA* 3.9 10.9 - - + +
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Residues in contact with GLY 87 (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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83A ILE 3.3 6.2 + - - -
84A PRO* 3.2 6.9 + - - -
86A PHE* 1.3 80.9 - - - +
88A ARG* 1.3 57.8 + - - +
90A THR* 3.4 3.0 - - - -
91A GLN* 3.0 34.8 + - - +
109A THR* 3.7 30.3 + - - -
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Residues in contact with ARG 88 (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 PRO* 3.2 33.0 + - - +
85A GLU* 3.2 44.2 + - - +
87A GLY* 1.3 76.2 - - - +
89A CYS* 1.3 59.7 + - - +
91A GLN* 3.4 8.6 + - - +
92A GLU* 2.8 36.7 + - - +
102A ILE* 5.3 5.7 - - + +
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Residues in contact with CYS 89 (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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85A GLU* 2.9 31.9 + - - +
86A PHE* 3.6 6.5 - - - +
88A ARG* 1.3 74.7 - - - +
90A THR* 1.3 57.7 + - - +
92A GLU* 3.3 17.4 + - - +
93A LEU* 2.8 36.0 + - - +
256A TYR* 4.3 1.8 - - - +
306A VAL* 5.4 1.3 - - + +
307A ALA* 4.7 6.5 - - - -
310A LEU* 3.7 46.5 - - + +
311A SER* 4.6 3.6 - - - -
316A ARG* 5.6 1.6 - - - +
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Residues in contact with THR 90 (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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86A PHE* 2.6 34.2 + - - -
87A GLY* 3.4 8.7 - - - -
89A CYS* 1.3 77.4 - - - +
91A GLN* 1.3 56.0 + - - -
93A LEU* 3.8 1.8 - - - +
94A LEU* 2.9 52.0 + - + +
109A THR* 4.1 7.2 - - + -
254A SER* 3.8 4.7 - - - +
256A TYR* 2.8 24.4 + - - +
269A ALA* 3.5 28.3 - - + -
271A THR* 4.4 1.1 - - - +
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Residues in contact with GLN 91 (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 GLY 3.0 20.4 + - - +
88A ARG* 3.4 7.1 + - - +
89A CYS 3.3 0.2 - - - -
90A THR* 1.3 75.8 - - - +
92A GLU* 1.3 64.5 + - - +
93A LEU 3.2 0.2 - - - -
94A LEU* 4.3 2.2 - - + +
95A PHE* 2.9 29.1 + - + +
102A ILE* 3.2 46.6 - - + +
107A ALA* 3.2 41.4 + - + +
108A ARG* 3.9 5.2 + - - +
109A THR* 3.0 29.9 + - - +
271A THR* 4.6 8.5 - - + +
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Residues in contact with GLU 92 (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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88A ARG* 2.8 23.3 + - - +
89A CYS* 3.5 17.4 - - - +
91A GLN* 1.3 73.0 - - - +
93A LEU* 1.3 59.6 + - - +
96A GLY* 2.8 36.9 + - - -
97A LYS* 4.0 32.4 + - + +
102A ILE* 4.0 4.0 - - + +
241A ARG* 4.2 0.2 + - - -
310A LEU 5.6 0.3 - - - +
316A ARG* 4.5 15.2 + - - +
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Residues in contact with LEU 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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89A CYS 2.8 16.7 + - - +
90A THR 3.9 3.6 - - - +
92A GLU* 1.3 76.5 - - - +
94A LEU* 1.3 56.4 + - + +
227A GLN* 3.1 38.0 + - - +
233A LEU* 4.0 29.8 - - + +
234A GLU* 5.6 0.7 - - - -
241A ARG* 2.9 19.2 + - - -
256A TYR* 3.9 31.0 - - + +
259A ASN* 5.2 2.5 - - - +
310A LEU* 4.7 10.1 - - + -
316A ARG* 3.7 27.6 - - - +
319A TRP* 4.8 8.1 - - + -
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Residues in contact with LEU 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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90A THR* 2.9 48.2 + - + +
91A GLN* 3.5 3.3 + - - +
93A LEU* 1.3 72.0 - - + +
95A PHE* 1.4 64.4 + - + +
224A PHE* 3.8 27.6 - - + -
227A GLN* 3.7 20.2 - - - +
237A ALA* 3.7 4.1 - - - +
240A LEU* 3.5 20.2 - - + +
241A ARG* 3.2 18.9 + - - +
252A VAL* 4.0 21.5 - - + -
254A SER* 4.1 15.7 - - - +
271A THR* 3.8 20.4 - - + +
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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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91A GLN* 2.9 28.9 + - + +
94A LEU* 1.4 78.7 - - + +
96A GLY* 1.3 59.8 + - - +
98A GLY 4.8 1.4 - - - +
99A SER* 3.2 29.5 + - - +
101A LEU* 3.8 34.3 - - + -
102A ILE* 4.4 3.6 - - + -
107A ALA* 4.3 8.1 - - + -
240A LEU* 3.7 28.3 - - + -
241A ARG* 3.4 23.6 + - + +
244A ALA* 3.9 16.8 - - + -
250A LEU* 4.4 0.9 - - + -
252A VAL* 4.2 17.3 - - + -
271A THR* 4.0 18.8 - - + -
273A VAL* 4.1 10.8 - - + -
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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