Contacts of the strand formed by residues 81 - 90 (chain D) in PDB entry 4JCQ
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 VAL 81 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 5.0 0.7 - - + -
53D ILE* 3.4 13.5 - - + +
55D ILE* 3.6 31.4 - - + -
74D ILE* 3.8 34.1 - - + +
77D ILE* 3.9 21.3 - - + -
79D PRO 3.6 11.1 + - - +
80D THR* 1.3 77.5 - - - +
82D LYS* 1.3 69.7 + - - +
83D VAL* 4.3 6.7 - - + -
100D ALA* 3.5 20.1 - - + +
101D GLU 4.9 0.2 + - - -
104D ASN* 3.6 11.4 + - - +
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Residues in contact with LYS 82 (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 PRO* 4.0 26.7 - - + +
53D ILE 2.8 12.2 + - - +
54D THR* 3.4 15.9 - - + +
55D ILE* 2.7 32.4 + - - -
80D THR* 4.0 8.2 + - + +
81D VAL* 1.3 77.0 - - - +
83D VAL* 1.3 58.8 + - - +
104D ASN* 3.5 33.1 + - + +
106D PHE* 4.1 22.2 - - + -
189D LEU* 4.4 17.7 - - + +
190D LYS 4.5 16.4 - - - -
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Residues in contact with VAL 83 (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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55D ILE* 3.3 14.8 - - + +
57D ILE* 4.0 18.6 - - + -
74D ILE* 5.2 3.1 - - + -
81D VAL* 4.2 7.4 - - + -
82D LYS* 1.3 78.1 - - - +
84D VAL* 1.3 61.0 + - - +
96D ILE 4.8 3.4 - - - +
97D TYR* 3.4 45.5 - - + +
100D ALA* 3.8 22.4 - - + +
104D ASN 3.0 7.6 + - - +
105D ARG* 3.8 12.3 - - + -
106D PHE* 2.8 36.1 + - - +
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Residues in contact with VAL 84 (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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54D THR* 4.0 22.9 - - + -
55D ILE 2.7 9.6 + - - +
56D PHE* 3.3 29.5 - - + -
57D ILE* 2.9 25.3 + - - -
83D VAL* 1.3 78.3 - - - +
85D GLY* 1.3 67.6 - - - +
86D THR* 3.7 1.6 + - - +
97D TYR* 4.4 1.8 - - - -
106D PHE* 3.4 6.7 - - + +
107D SER* 4.5 3.1 - - - -
108D LEU* 3.7 34.3 - - + +
183D ILE* 4.6 5.8 - - + -
189D LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 85 (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 3.7 6.3 - - - -
84D VAL* 1.3 72.3 - - - +
86D THR* 1.3 59.5 + - - -
89D VAL* 3.9 10.5 - - - -
97D TYR* 3.6 7.7 - - - -
106D PHE 3.0 12.9 + - - -
107D SER* 3.5 0.7 + - - -
108D LEU* 2.9 27.4 + - - +
111D THR* 3.3 8.8 + - - -
113D TYR* 3.4 16.6 - - - -
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Residues in contact with THR 86 (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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68C ASP 4.6 1.0 + - - -
69C THR* 2.8 44.8 + - + +
72C ASP* 4.7 0.5 + - - +
73C MET* 5.8 0.2 - - - -
27D TYR* 4.2 9.0 - - + +
56D PHE* 4.5 5.8 - - + -
57D ILE 2.9 23.4 + - - +
58D ASN* 3.2 24.9 - - + +
84D VAL 4.1 6.5 - - - +
85D GLY* 1.3 76.5 - - - -
87D GLY* 1.3 62.9 + - - +
88D TRP 3.0 8.8 + - - +
108D LEU* 3.8 26.0 - - + +
111D THR* 3.3 8.9 - - - +
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Residues in contact with GLY 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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65C GLU* 3.5 29.3 - - - +
68C ASP* 4.1 9.2 - - - +
69C THR* 3.6 1.8 + - - -
58D ASN* 3.9 1.3 - - - -
86D THR* 1.3 70.7 + - - +
88D TRP* 1.3 62.9 + - - +
110D ASN 3.3 20.5 + - - +
111D THR* 3.2 6.4 + - - -
112D ARG* 3.2 22.3 + - - +
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Residues in contact with TRP 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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32C GLN* 3.5 10.0 - - - +
65C GLU* 3.4 39.0 - - + +
131C ILE* 4.8 9.2 - - + -
58D ASN* 3.1 25.2 + - - -
59D SER 2.8 34.4 + - - -
60D GLN* 3.6 34.0 - - + +
86D THR 3.0 4.0 + - - -
87D GLY* 1.3 74.2 - - - +
89D VAL* 1.3 68.6 + - - +
111D THR* 4.1 1.1 - - - -
112D ARG* 3.3 45.3 - - + +
167D TRP* 3.6 32.5 - + + -
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Residues in contact with VAL 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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57D ILE* 3.6 26.9 - - + +
59D SER 3.4 3.4 - - - +
85D GLY* 3.9 13.0 - - - -
88D TRP* 1.3 79.9 - - - +
90D ALA* 1.3 59.2 + - - +
93D GLY* 3.5 30.1 - - - +
94D ILE* 3.5 17.8 - - + +
97D TYR* 3.9 13.0 - - + -
111D THR* 4.3 2.0 - - + -
112D ARG 3.0 7.2 + - - -
113D TYR* 3.3 31.2 - - + -
114D MET 3.1 20.4 + - - -
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Residues in contact with ALA 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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59D SER 2.9 8.3 + - - +
60D GLN* 3.7 16.4 - - - +
61D GLY* 3.4 9.5 + - - -
89D VAL* 1.3 76.0 - - - +
91D SER* 1.3 63.9 + - - +
92D ALA 3.2 1.0 + - - -
93D GLY* 2.8 23.9 + - - -
94D ILE* 3.8 3.6 - - - -
114D MET* 3.2 18.2 - - + +
167D TRP* 3.7 28.5 - - + -
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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