Contacts of the helix formed by residues 93 - 102 (chain D) in PDB entry 4U9W
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 LYS 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D TYR* 5.4 0.4 - - - -
90D TRP 4.0 15.3 - - - +
91D GLY 3.6 8.8 + - - +
92D TRP* 1.3 85.9 - - - +
94D ASP* 1.3 64.2 + - - +
95D ARG 3.4 2.0 - - - -
96D GLU* 3.2 28.3 + - + +
97D LYS* 3.2 13.8 + - - +
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Residues in contact with ASP 94 (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 PHE* 3.6 24.1 - - + -
78D LYS* 3.3 23.4 + - - +
92D TRP* 2.3 46.2 + - - +
93D LYS* 1.3 71.5 - - - +
95D ARG* 1.3 62.6 + - - +
97D LYS* 3.4 0.7 + - - +
98D ARG* 3.2 23.8 + - - +
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Residues in contact with ARG 95 (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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93D LYS 3.4 0.6 - - - -
94D ASP* 1.3 78.8 - - - +
96D GLU* 1.3 57.9 + - - +
98D ARG* 3.3 9.1 + - - +
99D GLU* 3.0 28.8 + - - +
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Residues in contact with GLU 96 (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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93D LYS* 3.2 29.4 + - + +
95D ARG* 1.3 81.0 - - - +
97D LYS* 1.3 59.3 + - - +
99D GLU* 3.6 8.1 - - - +
100D GLU* 3.2 21.5 + - - +
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Residues in contact with LYS 97 (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 PHE* 4.0 10.3 - - + -
77D THR* 4.8 2.9 - - + -
85D TYR* 3.0 35.7 + - - -
92D TRP* 3.8 28.5 - - + -
93D LYS 3.2 14.2 + - - +
94D ASP 3.9 3.8 - - - +
96D GLU* 1.3 75.0 - - - +
98D ARG* 1.3 60.4 + - - +
100D GLU* 2.6 31.6 + - - +
101D MET* 3.0 43.3 + - + +
139D GLU* 2.7 26.4 + - - +
2H GLY* 3.6 5.7 - - - -
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Residues in contact with ARG 98 (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 VAL* 6.2 1.6 - - + +
71D ASP* 4.5 18.8 + - - +
74D PHE* 3.1 58.3 - - + +
75D ASP* 4.5 4.4 + - - -
94D ASP* 3.2 15.5 + - - +
95D ARG* 3.8 8.8 - - - +
97D LYS* 1.3 73.4 - - - +
99D GLU* 1.3 59.3 + - - +
101D MET* 3.3 3.5 + - + +
102D THR* 2.6 50.9 + - + +
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Residues in contact with GLU 99 (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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95D ARG 3.0 17.3 + - - +
96D GLU* 3.6 10.3 - - - +
98D ARG* 1.3 75.2 - - - +
100D GLU* 1.3 58.9 + - - +
102D THR* 3.4 5.9 + - - -
103D ASP* 2.9 30.3 + - - +
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Residues in contact with GLU 100 (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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96D GLU 3.2 10.8 + - - +
97D LYS* 2.6 44.3 + - + +
99D GLU* 1.3 80.6 - - - +
101D MET* 1.3 62.3 + - - +
102D THR 3.3 0.9 + - - -
103D ASP* 3.4 4.8 + - - +
106D ALA* 4.4 0.3 - - - +
123D HIS* 3.5 6.8 + - + +
125D ARG* 2.8 28.8 + - - +
138D TYR* 3.7 36.3 - - + +
139D GLU* 4.2 1.0 - - - +
2H GLY* 3.7 5.7 - - - -
3H ARG* 4.2 12.0 + - - +
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Residues in contact with MET 101 (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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62D VAL* 3.6 5.4 - - - +
70D VAL* 4.9 3.5 - - + +
73D ALA* 3.6 5.4 - - + -
74D PHE* 3.6 39.3 - - + +
77D THR* 3.7 9.4 - - - +
97D LYS* 3.0 43.0 + - + +
98D ARG* 3.3 4.9 + - - +
100D GLU* 1.3 75.7 - - + +
102D THR* 1.3 62.1 + - + +
103D ASP 3.6 0.2 - - - -
106D ALA* 4.0 3.1 - - - +
108D TYR* 2.6 49.9 + - - +
121D PHE* 3.5 33.4 - - + -
123D HIS* 4.0 16.6 - - + +
139D GLU* 4.9 4.9 - - + +
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Residues in contact with THR 102 (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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62D VAL* 4.3 12.2 - - + +
70D VAL* 3.7 27.1 - - + -
98D ARG* 2.6 40.1 + - + +
99D GLU* 3.4 7.6 + - - -
101D MET* 1.3 80.4 - - + +
103D ASP* 1.3 66.6 + - - +
104D ASP* 3.5 4.7 + - - +
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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