Contacts of the helix formed by residues 87 - 94 (chain A) in PDB entry 2X1N
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 LEU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP* 1.3 71.3 - - - +
88A LYS* 1.3 61.0 + - - +
90A PHE* 3.2 14.9 + - + +
91A MET* 2.8 50.6 + - + +
99A ILE* 5.0 0.4 - - + -
107A TYR* 4.0 31.4 - - + -
130A PRO* 3.3 13.6 + - + +
133A LEU* 2.8 29.5 + - + +
135A ILE* 4.3 4.9 - - + +
141A ILE* 4.2 10.8 - - + -
192A ILE* 3.9 22.2 - - + -
196A MET* 3.7 25.4 - - + -
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Residues in contact with LYS 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 ASP* 2.9 8.6 + - - +
87A LEU* 1.3 79.1 - - - +
89A LYS* 1.3 61.5 + - + +
91A MET* 3.2 7.6 + - + +
92A ASP* 3.0 53.5 + - - +
130A PRO* 3.4 18.4 + - + +
131A GLN* 3.7 41.7 - - + +
167A TRP* 5.2 11.9 - - - -
168A TYR* 5.5 1.6 + - - -
195A GLU* 4.5 12.7 + - - +
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Residues in contact with LYS 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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10A ILE 5.4 0.6 + - - -
85A GLN* 3.4 25.6 - - - +
86A ASP* 2.7 31.2 + - - +
88A LYS* 1.3 77.5 - - + +
90A PHE* 1.3 61.7 + - - +
92A ASP* 3.3 12.4 + - + +
93A ALA* 2.9 30.5 + - - +
131A GLN* 6.0 2.2 - - - +
1297A X1N 2.9 24.9 + - + +
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Residues in contact with PHE 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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85A GLN* 3.7 17.2 + - - +
86A ASP 3.4 12.0 + - - +
87A LEU* 3.2 18.1 + - + +
89A LYS* 1.3 77.7 - - - +
91A MET* 1.3 57.4 + - - +
93A ALA* 3.3 5.1 + - + -
94A SER* 2.8 50.8 + - - -
99A ILE* 3.8 27.4 - - + -
100A PRO* 5.8 1.8 - - + -
103A LEU* 3.7 24.0 - - + -
107A TYR* 4.2 6.7 - + - -
135A ILE* 3.7 19.1 - - + -
294A PRO* 3.5 25.8 - - + -
295A HIS* 3.7 24.2 - - + -
296A LEU* 4.7 4.5 - - + -
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Residues in contact with MET 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 LEU* 2.8 41.2 + - + +
88A LYS* 3.6 6.3 - - + +
90A PHE* 1.3 74.8 - - - +
92A ASP* 1.3 61.1 + - - +
94A SER* 3.6 2.2 - - - +
95A ALA* 2.9 28.2 + - - +
99A ILE* 3.7 27.6 - - + -
130A PRO* 4.4 11.2 - - + -
192A ILE* 5.1 1.1 - - - +
195A GLU* 3.3 61.7 - - + +
196A MET* 3.8 11.2 - - + +
199A ARG* 5.6 3.8 - - - -
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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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88A LYS* 3.0 44.3 + - - +
89A LYS* 3.5 17.9 - - + +
91A MET* 1.3 77.6 - - - +
93A ALA* 1.3 59.3 + - - +
95A ALA* 3.2 19.4 - - - +
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Residues in contact with ALA 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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85A GLN* 5.5 2.9 - - - +
89A LYS 2.9 17.1 + - - +
90A PHE* 3.8 7.0 - - + +
92A ASP* 1.3 75.9 - - - +
94A SER* 1.3 59.5 + - - +
95A ALA 3.2 4.4 + - - +
96A LEU* 5.4 2.9 - - - +
97A THR* 4.9 1.0 + - - -
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Residues in contact with SER 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 PHE* 2.8 44.5 + - - -
91A MET 3.6 2.9 - - - -
93A ALA* 1.3 75.8 - - - +
95A ALA* 1.3 56.5 + - - +
97A THR* 3.2 7.7 + - - -
98A GLY* 2.7 42.6 + - - -
99A ILE* 3.9 22.2 - - - +
100A PRO* 6.2 0.2 - - - -
295A HIS 5.1 0.9 + - - -
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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