Contacts of the helix formed by residues 87 - 96 (chain D) in PDB entry 1XPM
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 ALA 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C LYS* 3.4 26.0 - - - +
109C GLU* 2.9 19.7 + - + +
85D ALA 3.3 2.4 + - - -
86D LYS* 1.3 71.4 - - - +
88D ALA* 1.3 55.8 + - - +
89D ALA 3.0 4.9 - - - +
90D VAL* 3.0 15.4 + - + +
91D GLN* 2.8 22.5 - - - +
105D PHE* 3.7 22.7 - - - +
106D GLU* 3.5 12.3 - - + +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 4.0 18.6 - - + -
52D VAL* 4.0 18.4 - - + -
76D VAL* 4.2 16.4 - - + -
82D VAL* 5.6 2.5 - - + -
86D LYS 3.5 1.8 + - - -
87D ALA* 1.3 70.3 - - - +
89D ALA* 1.3 62.5 + - - +
90D VAL 3.1 0.6 + - - -
91D GLN* 3.2 17.1 + - - +
92D ILE* 3.1 27.3 + - + +
106D GLU* 2.8 19.7 + - - +
138D THR* 5.7 0.7 - - + -
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 3.4 33.1 - - + +
76D VAL* 3.6 22.4 - - + +
87D ALA* 3.0 1.0 - - + +
88D ALA* 1.3 79.4 - - - +
90D VAL* 1.3 56.8 + - - +
92D ILE* 4.5 1.1 - - - -
93D HIS* 2.9 30.8 + - - +
104D CYS* 3.9 4.9 - - + -
105D PHE* 3.5 28.5 - - - +
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLU* 4.1 15.0 - - - +
179C THR* 4.0 12.3 - - + +
181C ASP* 3.9 17.2 - - - +
308C GLY 3.4 28.7 - - - +
310C VAL* 3.9 26.0 - - + -
86D LYS* 4.0 5.8 - - + -
87D ALA* 3.0 16.7 + - + +
89D ALA* 1.3 77.4 - - - +
91D GLN* 1.3 66.2 + - - +
93D HIS* 3.3 6.7 + - - +
94D ASN* 3.1 21.1 + - - +
104D CYS* 4.0 10.8 - - + -
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Residues in contact with GLN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.5 19.3 - - - +
183C TYR* 4.0 18.2 + - - +
52D VAL* 3.8 34.5 - - + +
82D VAL* 5.0 9.3 - - - +
83D ASP* 5.9 2.0 - - - +
86D LYS* 3.4 26.2 + - - +
87D ALA 2.8 25.3 - - - +
88D ALA* 3.2 13.0 + - - +
90D VAL* 1.3 72.7 - - - +
92D ILE* 1.3 58.6 + - - +
94D ASN* 3.1 3.6 + - - +
95D LEU* 2.8 34.9 + - + +
382D ARG* 6.2 1.0 - - - +
384D TYR* 5.0 11.7 + - + -
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE 4.4 2.2 - - - +
52D VAL* 3.8 37.2 - - + +
55D GLY* 4.1 15.7 - - - -
56D ALA* 4.4 8.1 - - + +
74D VAL* 4.8 5.2 - - + -
76D VAL* 3.9 25.8 - - + -
88D ALA* 3.1 16.3 + - + +
89D ALA* 4.0 5.2 - - - +
91D GLN* 1.3 76.1 - - - +
93D HIS* 1.3 63.4 + - - +
95D LEU* 4.4 6.1 - - - +
96D LEU* 2.9 48.3 + - + +
136D ILE* 3.7 19.3 - - + -
138D THR* 5.2 0.4 - - + -
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Residues in contact with HIS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C THR* 4.0 23.8 - - - +
180C GLU* 6.0 0.2 - - - -
74D VAL* 4.0 11.2 - - + +
89D ALA 2.9 20.1 + - - +
90D VAL* 3.5 4.9 + - - +
92D ILE* 1.3 76.1 - - - +
94D ASN* 1.3 67.2 + - - +
96D LEU 3.7 0.5 + - - -
97D GLY* 3.3 15.6 + - - -
98D ILE* 3.3 54.5 + - + +
99D GLN 2.8 24.0 + - - -
100D PRO* 4.1 12.9 - - + +
102D ALA* 4.2 7.9 - - + +
104D CYS* 3.5 22.7 - - - -
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Residues in contact with ASN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.2 40.7 + - + +
90D VAL 3.1 9.7 + - - +
91D GLN 3.1 8.4 + - - +
93D HIS* 1.3 80.6 + - - +
95D LEU* 1.3 68.4 + - - +
97D GLY* 3.1 13.7 + - - -
386D ARG* 4.1 20.1 + - - +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.7 30.7 - - + +
56D ALA* 4.2 13.5 - - + -
91D GLN* 2.8 20.9 + - + +
92D ILE* 3.8 4.5 - - - +
94D ASN* 1.3 76.3 - - + +
96D LEU* 1.3 60.4 + - - +
97D GLY 3.5 0.3 + - - -
372D PHE* 3.6 45.0 - - + -
384D TYR* 4.1 30.3 - - + -
386D ARG* 3.7 39.3 + - - +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA* 3.9 22.2 - - + +
59D ALA* 3.8 12.3 - - + -
60D LYS* 4.1 21.1 - - + -
63D ILE* 5.0 8.7 - - + -
68D LYS* 3.0 33.1 + - - +
92D ILE* 2.9 40.2 + - + +
95D LEU* 1.3 75.9 - - - +
97D GLY* 1.3 60.9 + - - +
98D ILE* 3.4 16.2 + - + -
134D LEU* 3.7 25.8 - - + -
372D PHE* 4.3 11.7 - - + -
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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