Contacts of the helix formed by residues 89 - 99 (chain A) in PDB entry 2CUY
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLY* 5.2 2.2 - - - -
9A GLN* 5.5 5.8 + - - +
87A GLY 3.4 0.4 + - - -
88A HIS* 1.3 78.2 + - - +
90A LEU* 1.3 69.5 + - - +
92A GLU* 3.0 12.1 + - - +
93A TRP* 3.9 2.8 - - - -
114A ARG* 2.8 22.6 + - - -
118A MET* 5.2 0.5 - - - +
194A HIS* 2.7 31.4 + - - -
224A ASN* 2.8 22.6 + - - -
243A GLN* 3.1 20.7 + - - +
248A VAL* 4.5 1.1 - - - +
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Residues in contact with LEU 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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7A PRO 3.9 11.2 - - - +
8A GLY* 4.4 8.5 - - - -
9A GLN* 4.9 4.7 - - + +
60A GLN* 3.7 45.1 - - + +
63A LEU* 3.9 15.5 - - + -
64A LEU* 4.1 3.4 - - + +
88A HIS 3.0 0.8 + - - -
89A SER* 1.3 81.1 + - - +
91A GLY* 1.3 65.5 + - - +
93A TRP* 3.0 21.0 + - + +
94A THR* 3.5 16.6 + - - +
111A VAL* 3.4 38.8 - - + -
114A ARG* 3.9 15.5 - - - +
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Residues in contact with GLY 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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6A PHE* 3.3 23.7 - - - +
7A PRO 3.4 9.8 + - - -
87A GLY* 3.2 13.5 - - - -
88A HIS 2.9 9.6 + - - -
90A LEU* 1.3 80.7 - - - +
92A GLU* 1.3 62.1 + - - +
94A THR* 3.1 11.7 + - - -
95A ALA 3.0 18.7 + - - -
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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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87A GLY* 3.4 18.5 - - - +
89A SER 3.0 3.7 + - - +
91A GLY* 1.3 76.5 - - - +
93A TRP* 1.3 62.6 + - - +
95A ALA* 3.3 3.0 + - - +
96A HIS* 3.1 43.1 + - + -
221A VAL* 4.8 1.1 - - + -
222A TYR 3.5 21.6 - - - +
223A SER* 3.5 16.5 + - - -
224A ASN* 2.8 30.4 + - - -
239A LEU* 4.8 7.8 - - - +
240A LEU* 3.8 16.5 - - + +
243A GLN* 2.9 31.5 + - - +
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Residues in contact with TRP 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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64A LEU* 3.8 16.8 - - + -
89A SER 3.9 10.1 - - - -
90A LEU* 3.0 20.9 + - - +
92A GLU* 1.3 79.0 - - + +
94A THR* 1.3 62.2 + - - +
96A HIS* 3.1 10.7 + - - +
97A VAL* 3.0 24.8 + - - +
102A LEU* 3.4 25.3 - - + +
107A ALA* 5.0 1.1 - - - -
110A LEU* 3.5 33.4 - - + -
111A VAL* 3.8 17.3 - - + -
114A ARG* 3.5 23.2 - - + +
205A LEU* 3.9 29.4 - - + -
209A LEU* 4.1 14.8 - - + -
240A LEU* 4.0 47.9 + - + +
243A GLN* 4.4 5.2 + - - -
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Residues in contact with THR 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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6A PHE* 3.4 30.8 - - + +
7A PRO 4.9 0.5 + - - -
63A LEU 4.5 0.9 + - - +
64A LEU* 3.4 51.4 - - + +
67A GLY* 4.0 2.7 - - - -
68A TYR* 3.8 12.3 - - + +
90A LEU* 3.5 14.9 + - - +
91A GLY* 3.1 10.1 + - - -
93A TRP* 1.3 76.0 - - - +
95A ALA* 1.3 66.0 + - - +
97A VAL* 3.1 4.6 + - - +
98A ALA* 2.9 21.8 + - - +
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Residues in contact with ALA 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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6A PHE* 3.6 26.4 - - + -
85A ALA* 4.3 3.1 - - + -
86A ALA 4.0 18.4 - - - +
91A GLY 3.0 12.0 + - - +
92A GLU 3.5 9.9 - - - +
94A THR* 1.3 76.8 - - - +
96A HIS* 1.3 58.3 + - - +
98A ALA* 3.1 3.8 + - - +
99A ALA* 2.9 29.3 + - - +
219A PHE* 4.5 1.9 - - - -
221A VAL* 3.8 20.9 - - + +
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Residues in contact with HIS 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 GLU* 3.1 40.7 + - + +
93A TRP* 3.1 11.4 + - - +
95A ALA* 1.3 74.1 - - - +
97A VAL* 1.3 62.6 + - - +
99A ALA* 3.4 2.9 + - - +
100A GLY 3.1 3.3 + - - -
101A THR* 2.8 58.8 + - + +
102A LEU* 3.5 12.1 + - + -
217A PRO* 5.2 1.3 - - + -
221A VAL* 3.4 33.3 + - + +
222A TYR 4.8 1.0 + - - -
230A GLU* 4.8 0.9 - - - +
236A ILE* 3.6 41.9 - - + +
240A LEU* 4.2 14.8 - - + +
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Residues in contact with VAL 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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64A LEU* 4.2 11.4 - - + -
68A TYR* 3.8 41.3 + - + -
93A TRP 3.0 17.8 + - - +
94A THR* 3.1 7.2 + - - +
96A HIS* 1.3 75.9 - - - +
98A ALA* 1.3 65.2 + - - +
100A GLY* 3.0 14.4 + - - -
102A LEU* 3.7 19.7 - - + +
104A LEU* 3.9 20.9 - - + +
107A ALA* 3.3 33.7 - - + -
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Residues in contact with ALA 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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6A PHE* 3.8 26.0 - - + -
68A TYR* 3.7 17.2 + - + -
71A TYR* 3.8 29.0 + - + -
94A THR 2.9 12.9 + - - +
95A ALA 3.3 9.0 - - - +
97A VAL* 1.3 79.4 - - - +
99A ALA* 1.3 59.5 + - - +
100A GLY 3.4 0.7 + - - -
218A ARG* 5.6 1.9 - - - +
219A PHE* 3.8 13.4 - - + -
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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 ALA 2.9 12.6 + - - +
96A HIS 3.4 4.0 + - - +
97A VAL 3.2 0.2 - - - -
98A ALA* 1.3 74.7 - - - +
100A GLY* 1.3 61.2 + - - +
216A ARG 4.5 0.3 - - - +
217A PRO* 3.5 24.8 - - + +
218A ARG* 2.7 34.5 + - - +
219A PHE* 3.5 33.4 - - + -
221A VAL* 3.6 8.1 - - + -
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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