Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 4ASQ
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 2.9 17.6 + - - -
88A TYR* 3.5 0.6 - - - +
89A GLN* 1.3 75.5 - - - +
91A GLU* 1.3 62.5 + - - +
92A ASP* 3.3 11.8 + - - +
93A LEU* 3.1 34.7 + - - +
94A LYS* 3.1 26.8 + - - +
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Residues in contact with GLU 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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89A GLN 3.3 7.9 + - - +
90A SER* 1.3 71.0 - - - +
92A ASP* 1.3 57.1 + - - +
94A LYS* 2.9 33.6 + - - +
95A ARG* 3.0 29.5 + - - +
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Residues in contact with ASP 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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90A SER* 3.2 9.5 + - - +
91A GLU* 1.3 75.7 - - - +
93A LEU* 1.3 70.4 + - - +
95A ARG* 3.3 2.1 + - - +
96A GLN* 3.1 26.4 + - - +
382A PRO* 6.0 0.2 - - - +
385A TYR* 2.7 59.6 + - - -
561A SER* 4.8 3.2 - - - +
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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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22A GLU* 3.6 45.8 - - + +
25A ALA* 5.0 0.7 - - + -
26A LYS* 4.1 35.0 - - + +
29A LEU* 3.9 23.1 - - + -
88A TYR* 4.5 11.9 - - + -
90A SER* 3.1 24.2 + - - +
92A ASP* 1.3 86.1 - - - +
94A LYS* 1.3 62.9 + - - +
96A GLN* 3.3 8.0 + - - +
97A PHE* 3.0 30.8 + - + -
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Residues in contact with LYS 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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85A TRP* 3.1 43.8 - - + +
86A ARG* 4.0 15.3 + - - +
88A TYR* 3.4 29.7 + - + +
89A GLN 4.5 0.8 + - - -
90A SER 3.1 19.0 + - - +
91A GLU* 2.9 38.5 + - - +
93A LEU* 1.3 75.2 - - - +
95A ARG* 1.3 57.4 + - - +
97A PHE* 3.4 1.2 + - - -
98A LYS* 2.9 30.8 + - - +
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Residues in contact with ARG 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 GLU 3.0 18.8 + - - +
92A ASP* 4.5 0.9 - - - +
94A LYS* 1.3 76.5 - - - +
96A GLN* 1.3 61.7 + - - +
98A LYS* 3.5 8.7 + - + +
99A ALA* 3.1 23.0 + - - +
209A GLU* 2.7 43.2 + - - -
385A TYR* 3.4 17.7 - - + +
389A ALA 5.2 1.2 + - - -
560A ALA* 3.0 32.7 + - - +
561A SER 3.2 21.8 + - - -
562A LYS* 3.5 16.1 + - - +
563A PRO* 3.7 21.0 - - - +
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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
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29A LEU* 3.9 28.8 - - + +
33A ASN* 2.9 26.7 - - - +
92A ASP* 3.1 33.2 + - - +
93A LEU* 3.6 11.9 - - - +
95A ARG* 1.3 74.1 - - - +
97A PHE* 1.3 64.4 + - - +
99A ALA* 3.3 6.1 + - - +
100A LEU* 3.1 28.0 + - + +
382A PRO* 3.9 14.7 - - - +
384A VAL* 3.8 17.1 - - + +
385A TYR* 3.3 27.0 - - + +
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Residues in contact with PHE 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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25A ALA* 3.8 19.3 - - + -
28A TYR* 3.9 25.8 - + - -
29A LEU* 3.7 24.7 - - + -
80A THR* 3.9 21.3 - - + -
83A PHE* 3.7 41.3 - + + -
85A TRP* 3.5 37.5 - + + -
88A TYR* 4.1 8.1 - + - -
93A LEU* 3.0 26.6 + - + +
94A LYS 3.8 1.6 - - - +
96A GLN* 1.3 71.8 - - - +
98A LYS* 1.3 65.5 + - - +
100A LEU* 3.1 17.0 + - + +
101A THR* 3.2 18.9 + - - +
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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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85A TRP* 3.9 25.9 - - + -
94A LYS 2.9 18.1 + - - +
95A ARG* 3.6 9.9 - - + +
97A PHE* 1.3 75.1 - - - +
99A ALA* 1.3 62.6 + - - +
101A THR* 2.6 26.9 + - - +
102A LYS* 3.5 38.5 + - - +
206A ASP* 5.0 3.2 + - - -
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Residues in contact with ALA 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 ARG 3.1 13.4 + - - +
96A GLN* 3.3 10.7 + - - +
98A LYS* 1.3 75.9 - - - +
100A LEU* 1.3 61.2 + - - +
102A LYS* 3.3 29.3 + - - +
384A VAL* 4.1 26.7 - - + +
385A TYR* 5.9 1.8 - - + -
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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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28A TYR* 4.7 0.9 - - + -
29A LEU* 3.5 31.2 - - + -
32A LEU* 3.7 18.4 - - + -
33A ASN* 5.3 2.2 - - - +
36A LEU* 3.6 31.4 - - + -
73A MET* 5.1 10.7 - - + +
76A VAL* 3.9 15.9 - - + +
77A ALA* 3.9 18.0 + - - +
80A THR* 3.9 17.7 - - + -
96A GLN 3.1 12.2 + - - +
97A PHE* 3.1 14.2 + - + +
99A ALA* 1.3 73.4 - - - +
101A THR* 1.3 63.6 + - - +
102A LYS 3.5 3.4 + - - +
103A LEU* 5.0 2.8 - - - +
384A VAL* 3.9 16.2 - - + -
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Residues in contact with THR 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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77A ALA* 4.4 10.1 - - - +
80A THR* 3.6 21.5 - - - +
85A TRP* 4.0 24.5 - - + +
86A ARG* 5.4 3.1 - - - +
97A PHE 3.3 14.1 - - - +
98A LYS* 2.6 22.7 + - - +
100A LEU* 1.3 78.0 - - - +
102A LYS* 1.3 64.5 + - - +
103A LEU* 3.3 15.3 + - - +
195A ASN* 4.6 2.8 - - - +
1B NAG 5.2 9.7 - - - +
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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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73A MET* 5.5 5.2 - - - +
98A LYS* 3.5 49.0 - - - +
99A ALA* 3.3 18.9 + - - +
100A LEU 3.3 3.0 - - - +
101A THR* 1.3 78.4 - - - +
103A LEU* 1.3 62.9 + - - +
104A GLY 3.5 2.2 - - - +
195A ASN* 4.7 3.1 - - - -
197A PHE* 5.4 10.8 - - + -
206A ASP* 2.7 36.1 + - - +
207A GLU* 5.8 3.4 - - - +
209A GLU* 5.6 6.1 - - - +
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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