Contacts of the strand formed by residues 66 - 72 (chain D) in PDB entry 3I54
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 GLU 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D LYS* 4.3 14.6 + - - -
58D GLY* 3.9 2.9 - - - -
59D ARG 3.5 17.4 - - - +
60D ARG* 4.8 2.0 - - - +
61D ALA* 5.0 1.6 - - - -
64D GLY 5.2 0.9 - - - +
65D ARG* 1.3 78.9 - - - +
67D ASN* 1.3 71.5 + - - +
68D LEU* 3.8 19.8 - - + +
92D SER* 3.6 19.9 + - - -
94D THR* 5.4 2.1 + - - -
182D GLN* 3.3 43.2 + - - +
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Residues in contact with ASN 67 (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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138C LEU* 6.0 5.8 - - - -
142C ILE* 6.1 6.1 - - + -
143C PHE* 6.1 4.9 - - + -
58D GLY* 3.2 2.4 - - - -
59D ARG* 2.7 46.4 + - - +
61D ALA* 4.9 5.9 - - + +
65D ARG 4.3 0.2 + - - -
66D GLU* 1.3 74.2 - - - +
68D LEU* 1.3 66.8 + - - +
69D LEU* 3.6 25.7 + - - -
182D GLN* 3.8 9.6 - - - +
185D GLY* 5.9 4.5 - - - -
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Residues in contact with LEU 68 (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 LYS* 4.0 30.1 - - + -
57D ILE 3.2 13.7 - - - +
58D GLY* 3.8 10.3 - - - -
66D GLU* 3.8 22.4 - - - +
67D ASN* 1.3 76.8 - - - +
69D LEU* 1.3 63.3 + - - +
70D THR 3.4 0.7 - - - +
71D ILE* 4.6 10.1 - - + -
175D LEU* 5.0 0.4 - - + -
179D GLU* 3.6 32.8 - - + +
182D GLN* 3.2 36.6 + - + +
183D LEU* 3.6 29.4 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ASN* 3.7 14.6 - - + +
138C LEU* 6.0 7.9 - - + -
57D ILE* 2.7 23.4 + - + +
59D ARG* 3.5 36.6 - - + +
67D ASN* 3.6 24.7 - - - +
68D LEU* 1.3 73.6 - - - +
70D THR* 1.3 63.6 + - - +
91D SER* 3.6 9.0 - - - +
137D ASN* 3.9 20.1 + - - -
183D LEU* 4.4 2.4 - - - +
301D CMP 3.5 41.1 + - + +
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Residues in contact with THR 70 (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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57D ILE* 3.1 46.3 + - + +
68D LEU 3.4 1.6 - - - -
69D LEU* 1.3 80.5 - - - +
71D ILE* 1.3 81.0 + - - +
72D MET* 4.0 11.4 - - + -
133D ARG* 5.3 10.0 + - - -
183D LEU* 3.9 8.5 - - - +
301D CMP 3.6 32.1 - - + +
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D LYS* 4.3 4.7 - - + -
55D VAL 3.4 5.8 - - - +
56D LYS* 3.5 25.1 - - + -
68D LEU* 4.6 3.8 - - + -
70D THR* 1.3 94.5 + - - +
72D MET* 1.3 70.1 + - - +
73D GLY 4.2 0.5 + - - -
76D ASP* 4.4 2.9 - - - +
96D ILE* 4.0 18.4 - - + -
157D LEU* 4.4 7.4 - - + +
161D PHE* 4.0 30.0 - - + -
173D HIS 4.9 2.5 - - - +
175D LEU* 3.9 22.7 - - + -
183D LEU* 3.7 30.5 - - + +
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Residues in contact with MET 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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50D ILE* 3.5 19.1 - - + -
54D LYS* 3.1 9.4 - - - +
55D VAL* 2.7 38.1 + - + +
57D ILE* 3.1 30.7 - - + -
70D THR* 4.0 8.3 - - + -
71D ILE* 1.3 72.8 - - - +
73D GLY* 1.3 58.8 + - - +
76D ASP* 3.5 18.2 - - + +
77D MET 3.5 19.1 - - - +
78D PHE* 3.7 19.3 - - + -
130D ARG* 3.5 30.5 - - - +
161D PHE* 4.4 3.1 - - - -
301D CMP 3.7 17.9 - - - +
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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