Contacts of the strand formed by residues 86 - 93 (chain D) in PDB entry 1PXV
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 HIS 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TRP* 3.7 1.4 - - - -
82D ASP* 3.0 43.2 + - + +
83D ASP* 2.9 37.5 + - - +
84D THR 3.7 0.4 - - - -
85D GLN* 1.3 101.9 + - + +
87D ILE* 1.3 65.0 + - - +
88D LEU* 5.5 0.2 - - + -
104D VAL* 4.2 19.5 - - + -
105D TYR 3.3 6.5 - - - +
106D GLU* 3.9 24.3 + - + +
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Residues in contact with ILE 87 (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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26D LEU 4.4 4.3 - - - +
27D PHE* 3.8 27.8 - - + -
31D TRP* 3.6 56.3 - - + +
40D ILE* 4.3 4.0 - - + -
42D ILE* 4.1 8.5 - - + -
79D LEU* 3.9 22.9 - - + -
80D ASP 3.3 11.0 - - - +
81D TYR* 4.3 8.7 - - + -
86D HIS* 1.3 79.3 - - - +
88D LEU* 1.3 66.2 + - - +
104D VAL* 3.6 2.8 - - - +
105D TYR* 2.7 39.8 + - + +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 5.7 2.7 - - + -
380B PHE* 3.8 26.9 - - + -
382B ARG* 4.1 17.2 + - - +
78D ILE 3.5 1.4 - - - +
79D LEU* 3.2 7.8 - - - -
80D ASP* 2.9 46.5 + - + +
81D TYR 5.0 0.2 - - - -
82D ASP* 3.8 26.9 - - + +
86D HIS 4.9 0.4 - - - -
87D ILE* 1.3 79.7 - - - +
89D MET* 1.3 61.2 + - - +
102D PRO* 4.0 11.4 - - + -
103D ILE 3.2 5.8 - - - +
104D VAL* 3.8 29.4 - - + -
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Residues in contact with MET 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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5D GLN* 3.6 23.8 - - - +
7D ILE* 4.5 12.3 - - - -
38D LYS* 3.9 4.9 - - - +
40D ILE* 3.8 18.6 - - + -
67D PHE* 4.9 2.9 - - - -
77D TYR* 4.5 17.0 - - + -
78D ILE 3.3 6.1 - - - +
79D LEU* 3.7 23.6 - - + -
87D ILE 4.3 0.2 - - - -
88D LEU* 1.3 75.3 - - - +
90D GLN* 1.3 72.9 + - - +
91D THR* 5.5 2.7 - - + -
102D PRO* 3.6 1.2 - - - +
103D ILE* 2.9 37.5 + - - +
105D TYR* 3.7 35.8 - - + +
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Residues in contact with GLN 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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338B LEU* 3.8 18.4 - - - +
362B TRP* 3.3 24.5 - - - -
382B ARG* 3.0 23.7 + - - +
384B TYR* 4.3 1.6 + - - -
77D TYR* 3.4 4.0 - - - -
78D ILE* 2.8 44.2 + - + +
88D LEU 5.7 0.2 - - - -
89D MET* 1.3 79.1 - - - +
91D THR* 1.3 68.2 + - - +
99D THR* 3.4 21.0 - - + +
100D SER* 2.9 29.9 + - - +
102D PRO* 3.5 19.0 - - + +
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Residues in contact with THR 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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239B ASP 5.1 1.6 - - - -
240B ASN* 4.8 3.5 + - - -
241B SER* 4.3 8.0 + - - -
281B ASN* 4.2 18.2 + - - +
75D ILE* 4.4 7.9 - - + -
76D ILE 3.3 5.4 - - - +
77D TYR* 3.5 37.2 - - + -
78D ILE* 4.0 1.3 - - - -
89D MET* 5.5 3.1 - - + -
90D GLN* 1.3 75.2 - - - +
92D SER* 1.3 61.4 + - - +
99D THR* 3.4 5.5 - - - +
100D SER* 2.9 46.0 + - - +
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Residues in contact with SER 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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241B SER* 4.5 5.5 + - - -
281B ASN 5.8 0.6 - - - +
338B LEU* 3.7 35.3 - - - -
339B GLY 3.8 2.3 + - - -
75D ILE* 3.6 8.1 - - - +
76D ILE* 2.8 30.0 + - - -
78D ILE* 3.9 5.8 - - - -
91D THR* 1.3 77.6 - - - +
93D SER* 1.3 70.0 + - - +
96D GLY 5.7 0.2 + - - -
98D GLY 3.5 9.0 + - - -
99D THR* 3.0 22.3 + - - -
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Residues in contact with SER 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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241B SER* 5.5 0.4 - - - -
281B ASN 5.7 3.1 - - - -
283B ALA* 3.4 29.7 - - - +
285B PHE* 4.4 4.2 - - - -
337B HIS 4.4 7.1 - - - +
339B GLY 5.1 1.0 + - - -
74D GLU* 3.5 6.5 + - - +
76D ILE* 4.0 7.1 - - - +
92D SER* 1.3 84.9 + - - +
94D LYS* 1.3 64.4 + - - +
95D GLN 3.4 1.2 + - - -
96D GLY* 2.6 44.7 + - - +
98D GLY 3.6 4.2 + - - -
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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