Contacts of the helix formed by residues 87 - 95 (chain A) in PDB entry 1XJP
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 ILE 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE 3.1 8.1 + - - +
84A LYS* 3.8 8.1 - - - +
85A ASP 4.5 2.9 - - - -
86A GLY* 1.3 68.2 - - - +
88A TYR* 1.4 58.2 + - - +
89A PHE* 5.6 0.2 - - - -
90A ALA* 2.2 44.6 - - + +
91A ALA* 2.3 57.9 + - + +
94A LYS* 3.8 23.1 - - + -
205A VAL* 2.6 36.3 - - + +
208A ASP* 4.7 6.5 - - + +
209A LEU* 4.2 10.1 - - + +
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Residues in contact with TYR 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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86A GLY 2.7 20.7 + - - -
87A ILE* 1.4 71.6 - - - +
89A PHE* 1.3 102.6 + + + +
90A ALA 3.4 0.5 + - - -
92A THR* 3.2 24.6 + - - -
203A ILE* 4.8 3.6 - - + +
205A VAL* 6.2 0.2 - - + -
206A VAL* 6.1 1.1 - - + -
364A PHE* 3.8 31.4 + - + +
365A LYS* 4.1 16.6 - - + -
366A CYS* 3.3 21.1 - - + -
377A LEU* 3.2 20.4 + - - +
378A CYS* 3.2 27.3 - - - -
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Residues in contact with PHE 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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87A ILE 5.3 0.2 - - - -
88A TYR* 1.3 111.0 - + + +
90A ALA* 1.3 59.3 + - + +
92A THR* 4.8 5.7 - - - -
93A GLU* 5.1 5.4 + - - +
206A VAL* 3.5 35.9 - - + -
209A LEU* 5.8 6.3 - - + -
338A TYR* 6.1 0.7 - - - -
448A LEU* 6.6 0.4 - - + -
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Residues in contact with ALA 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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87A ILE* 2.2 48.8 - - + +
88A TYR 3.3 0.2 - - - -
89A PHE* 1.3 82.9 - - + +
91A ALA* 1.4 48.4 + - - +
92A THR 3.1 7.9 + - - -
93A GLU* 3.1 7.8 + - - +
94A LYS* 2.6 29.8 + - - +
205A VAL* 4.5 1.1 - - + -
206A VAL* 4.8 0.9 - - + -
209A LEU* 3.8 28.5 - - + +
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Residues in contact with ALA 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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84A LYS* 4.1 11.9 - - + +
87A ILE* 2.3 56.7 + - + +
90A ALA* 1.4 64.7 - - - +
92A THR* 1.3 51.1 + - - +
94A LYS* 3.5 16.6 - - + -
95A SER* 2.7 36.5 + - - +
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Residues in contact with THR 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 TYR 3.2 19.5 + - - -
89A PHE 4.8 4.9 - - - -
90A ALA 3.1 1.0 + - - -
91A ALA* 1.3 75.3 - - - +
93A GLU* 1.3 60.2 + - + +
95A SER* 3.0 9.9 + - - -
96A ASN* 2.6 30.8 + - - +
452A GLU* 4.1 30.3 - - + +
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Residues in contact with GLU 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 PHE 5.3 4.9 - - - +
90A ALA* 3.1 7.7 + - - +
92A THR* 1.3 80.6 - - + +
94A LYS* 1.4 59.1 + - - +
95A SER 3.2 1.8 - - - -
96A ASN* 3.0 9.7 + - - +
97A VAL* 3.0 26.3 + - - +
98A VAL* 3.0 23.1 + - + +
209A LEU* 6.1 1.3 - - + -
451A PHE* 2.3 45.3 - - - +
452A GLU* 3.4 35.5 - - + +
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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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84A LYS* 2.3 46.6 - - + +
87A ILE* 3.8 24.0 - - + -
90A ALA* 2.6 23.8 + - + +
91A ALA* 3.5 11.2 - - + -
93A GLU* 1.4 70.5 - - - +
95A SER* 1.3 56.3 + - - +
96A ASN 3.5 0.2 - - - -
98A VAL* 4.1 10.0 - - + +
99A ARG* 3.0 57.1 + - + +
208A ASP* 5.3 10.5 + - - +
209A LEU* 5.3 4.0 - - + +
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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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91A ALA* 2.7 27.1 + - - -
92A THR* 3.0 10.7 + - - -
93A GLU 3.2 0.2 - - - -
94A LYS* 1.3 75.2 - - - +
96A ASN* 1.3 65.3 + - - +
99A ARG* 3.7 18.9 + - - +
100A GLY 5.8 0.7 - - - -
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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