Contacts of the strand formed by residues 81 - 90 (chain D) in PDB entry 1GO4
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
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Residue Dist Surf HB Arom Phob DC
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72D LEU* 3.8 15.0 - - + -
75D TRP* 3.6 23.5 + - + +
76D LEU* 3.6 28.5 - - + -
79D CYS 3.3 0.7 - - - +
80D SER* 1.3 78.8 - - - +
82D GLN* 1.3 65.2 + - - +
83D LYS 3.9 8.1 - - - +
104D ILE* 3.7 34.6 - - + +
106D CYS* 3.4 21.8 - - - -
155D ILE* 3.9 7.2 - - + -
156D TYR 3.8 8.7 - - - +
157D THR* 4.5 2.5 - - - -
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Residues in contact with GLN 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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81D VAL* 1.3 76.6 - - - +
83D LYS* 1.3 76.1 + - + +
103D ASP* 3.7 1.0 - - - +
104D ILE* 2.9 27.8 + - - +
156D TYR* 2.7 21.4 + - + +
157D THR 3.0 21.2 + - - -
158D ASP* 3.0 27.4 + - - +
539H ARG* 3.2 17.6 + - - +
540H THR* 2.9 25.9 + - - +
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Residues in contact with LYS 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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81D VAL* 3.8 3.3 - - - +
82D GLN* 1.3 95.1 + - - +
84D LEU* 1.3 62.5 + - - +
101D GLN* 3.1 45.3 - - + +
102D PHE 3.5 6.5 - - - +
103D ASP* 3.4 27.3 + - + -
104D ILE* 4.1 6.5 - - - +
154D LEU 4.3 0.2 - - - -
155D ILE* 3.3 14.0 - - - +
156D TYR* 3.0 69.6 + - + +
530H ALA 5.3 2.2 + - - -
533H GLY 5.3 0.7 - - - -
534H ASP 4.9 7.4 + - - -
535H TYR* 5.3 1.4 - - - +
540H THR* 5.1 1.2 + - - +
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Residues in contact with LEU 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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24D PHE* 3.7 42.8 - - + -
28D ILE* 4.7 6.1 - - + -
68D VAL* 4.5 11.4 - - + -
72D LEU* 4.5 12.8 - - + -
83D LYS* 1.3 75.6 - - - +
85D VAL* 1.3 62.8 + - - +
86D VAL* 3.9 24.7 - - + -
102D PHE* 2.9 37.6 + - + -
104D ILE* 4.5 5.2 - - + -
153D LEU* 4.6 11.4 - - + -
154D LEU 3.2 9.9 - - - +
155D ILE* 3.6 29.8 - - + -
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Residues in contact with VAL 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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84D LEU* 1.3 80.1 - - - +
86D VAL* 1.3 63.4 + - - +
87D VAL* 3.8 9.6 + - + -
99D ARG* 3.7 38.1 - - + +
100D TRP 2.9 13.9 - - - +
101D GLN* 3.8 20.9 - - + +
152D ASP 3.4 3.5 - - - +
153D LEU* 3.4 3.1 - - - +
154D LEU* 2.6 49.3 + - + +
156D TYR* 3.4 33.2 - - + -
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Residues in contact with VAL 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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28D ILE* 4.4 15.0 - - + +
31D ILE* 4.9 14.6 - - + -
32D LEU* 5.1 5.8 - - + -
84D LEU* 3.9 13.7 - - + -
85D VAL* 1.3 74.6 - - - +
87D VAL* 1.3 60.8 + - - +
88D ILE* 4.0 14.7 + - + +
99D ARG* 3.8 2.1 - - - -
100D TRP* 2.7 45.6 + - + +
102D PHE* 4.3 14.4 - - + -
151D PHE* 3.7 27.4 - - + -
152D ASP 3.5 3.4 - - - -
153D LEU* 3.9 15.0 - - + -
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Residues in contact with VAL 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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85D VAL* 3.9 10.8 - - + -
86D VAL* 1.3 76.3 - - - +
88D ILE* 1.3 65.7 + - - +
89D SER* 4.1 4.2 + - - +
96D VAL* 3.5 37.5 - - + -
98D GLU 4.0 2.2 - - - -
99D ARG* 4.5 4.9 - - + +
151D PHE* 2.9 28.1 - - - +
152D ASP* 2.9 18.3 + - + +
154D LEU* 3.2 38.8 - - + -
173D GLN* 3.8 18.8 - - + +
550H THR* 4.8 0.3 + - - -
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Residues in contact with ILE 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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31D ILE* 6.0 3.8 - - + -
32D LEU* 5.1 1.3 - - + -
35D ARG* 5.6 3.6 - - + -
37D ILE* 3.6 31.9 - - + -
86D VAL* 4.2 14.1 - - + +
87D VAL* 1.3 74.7 - - - +
89D SER* 1.3 59.2 + - - +
96D VAL* 3.6 1.9 - - - +
97D LEU* 2.9 25.3 + - - +
98D GLU* 3.0 37.8 + - + +
100D TRP* 5.0 4.9 - - + +
145D LEU* 3.8 15.9 - - + -
149D CYS* 3.7 15.5 - - + -
150D SER 3.3 10.8 - - - +
151D PHE* 3.2 29.6 - - + -
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Residues in contact with SER 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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87D VAL* 4.0 5.3 + - - +
88D ILE* 1.3 75.0 - - - +
90D ASN* 1.3 69.3 + - - +
91D ILE* 3.2 0.9 + - - -
94D GLY 3.8 14.0 + - - -
95D GLU 3.2 16.6 - - - -
96D VAL* 4.0 8.5 - - - -
97D LEU* 4.4 0.7 - - - +
149D CYS* 3.3 7.6 - - - -
150D SER* 3.1 29.0 + - - -
173D GLN* 5.1 5.2 + - - -
550H THR* 4.0 25.1 + - - +
554H ARG* 4.2 3.1 + - - -
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Residues in contact with ASN 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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89D SER* 1.3 71.5 + - - +
91D ILE* 1.3 60.6 + - - +
92D GLU* 2.7 38.4 + - - +
93D SER* 3.0 27.4 + - - -
94D GLY* 2.9 32.2 + - - +
95D GLU* 2.9 23.0 + - + +
97D LEU* 4.6 8.4 - - + +
147D VAL* 3.4 28.5 - - - +
148D SER 4.0 4.5 - - - -
149D CYS* 4.5 7.9 - - - -
554H ARG* 4.0 2.6 + - - -
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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