Contacts of the strand formed by residues 71 - 77 (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 ILE 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ILE* 3.8 30.7 - - + -
67D ASP* 3.0 26.4 + - + +
68D LYS 4.3 0.4 + - - -
69D LYS 3.7 0.8 - - - -
70D LYS* 1.3 76.0 - - - +
72D GLY* 1.3 58.6 + - - +
73D MET 3.3 28.5 - - - +
74D VAL* 4.1 13.9 - - + -
98D ILE* 3.9 29.5 - - + +
99D GLN* 2.9 24.8 + - - +
102D ALA* 3.8 3.6 - - - +
132D LYS* 3.3 19.5 - - + +
133D VAL 5.1 0.4 - - - -
134D LEU* 4.1 15.9 - - + +
161D VAL* 5.5 2.9 - - + -
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Residues in contact with GLY 72 (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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70D LYS 3.2 4.0 + - - -
71D ILE* 1.3 71.7 - - - +
73D MET* 1.3 67.6 + - - +
99D GLN* 4.2 4.9 - - - -
101D PHE 4.3 3.1 - - - +
102D ALA* 3.1 11.8 - - - -
103D ARG* 3.0 21.0 + - - +
124D TYR* 4.1 6.8 + - - -
131D GLU* 3.5 22.6 + - - -
132D LYS 2.9 10.4 + - - -
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Residues in contact with MET 73 (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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120C LEU* 4.0 12.8 - - + -
71D ILE* 3.3 6.9 - - - +
72D GLY* 1.3 83.7 - - - +
74D VAL* 1.3 63.5 + - - +
75D ILE* 4.1 21.1 - - + -
102D ALA* 4.4 0.4 - - - -
103D ARG* 3.2 47.1 - - + +
105D PHE* 4.2 13.5 - - - -
121D ALA* 4.2 6.3 - - - +
124D TYR* 3.5 45.5 - - + -
132D LYS 4.1 2.6 + - - -
133D VAL* 3.6 17.9 - - + +
134D LEU 3.0 24.8 + - - -
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Residues in contact with VAL 74 (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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71D ILE* 4.1 6.3 - - + -
73D MET* 1.3 77.5 - - - +
75D ILE* 1.3 64.0 + - - +
76D VAL* 4.9 3.1 - - + -
89D ALA* 3.4 25.2 - - + +
92D ILE* 4.8 7.6 - - + -
93D HIS* 4.0 23.8 - - + +
98D ILE* 3.8 27.1 - - + -
102D ALA* 5.2 0.9 - - + -
103D ARG 2.8 8.5 + - - +
104D CYS* 3.3 13.7 - - - -
105D PHE 3.3 23.2 + - - -
134D LEU* 3.4 21.5 - - + +
136D ILE* 5.0 2.7 - - + -
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Residues in contact with ILE 75 (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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120C LEU* 5.0 1.3 - - + -
73D MET* 4.1 26.5 - - + -
74D VAL* 1.3 76.2 - - - +
76D VAL* 1.3 69.6 + - - +
77D ALA 4.1 0.3 + - - -
105D PHE* 3.4 38.1 - - + +
107D MET* 3.9 27.8 - - + -
117D ALA* 3.9 41.3 - - + +
120D LEU 5.9 0.2 - - - -
121D ALA* 5.2 0.9 - - - +
133D VAL* 4.3 7.2 - - + -
134D LEU 2.9 10.9 + - - +
135D VAL* 3.4 4.8 - - + +
136D ILE* 2.8 26.9 + - - +
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Residues in contact with VAL 76 (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* 4.9 3.6 - - + -
75D ILE* 1.3 78.8 - - - +
77D ALA* 1.3 67.4 - - - +
78D THR* 4.3 5.6 - - + -
88D ALA* 4.2 8.1 - - + -
89D ALA* 3.6 30.5 - - + +
92D ILE* 3.9 19.7 - - + -
105D PHE 3.1 7.1 + - - -
106D GLU* 3.1 25.3 - - + +
107D MET 2.9 23.5 + - - -
136D ILE* 3.2 10.3 - - + +
138D THR* 3.7 27.4 - - + -
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Residues in contact with ALA 77 (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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75D ILE 4.1 0.8 + - - -
76D VAL* 1.3 72.6 - - - +
78D THR* 1.3 61.6 + - - +
107D MET* 3.5 8.1 - - + +
113D ALA* 3.5 12.8 - - + +
114D ALA* 3.4 42.0 - - + +
117D ALA* 5.1 4.0 - - + -
135D VAL* 5.5 0.9 - - + -
136D ILE 2.8 12.7 + - - +
137D ALA* 4.3 0.4 - - - -
138D THR 3.0 25.5 + - - -
278D THR* 3.1 10.0 + - - -
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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