Contacts of the helix formed by residues 94 - 103 (chain D) in PDB entry 5XAC
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 PRO 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ASP 5.3 0.7 - - - +
57D HIS 5.1 4.0 - - - +
58D VAL 3.6 3.1 - - - +
59D ASN* 3.3 19.3 - - - +
92D SER 3.4 6.5 - - - +
93D THR* 1.3 90.6 - - + +
95D ILE* 1.3 65.7 + - - +
96D SER* 4.1 14.4 - - - +
97D GLU* 3.1 31.9 + - + +
98D VAL* 3.1 11.7 + - - +
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Residues in contact with ILE 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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31D ILE* 4.2 17.9 - - + -
33D VAL* 5.0 1.1 - - + -
54D VAL* 4.5 9.2 - - + -
55D PRO 3.4 24.7 - - - +
56D ASP 3.4 6.3 - - - +
58D VAL* 2.8 31.1 + - + +
59D ASN 4.8 2.9 - - - -
60D MET* 3.7 28.0 - - - -
63D LEU* 4.1 12.6 - - + -
93D THR 3.6 2.5 + - - -
94D PRO* 1.3 69.6 - - - +
96D SER* 1.3 62.1 + - - +
98D VAL* 3.2 6.0 + - + +
99D TYR* 2.8 29.2 + - - +
109D LEU* 4.0 12.8 - - + -
111D MET* 3.7 18.6 - - + -
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Residues in contact with SER 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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31D ILE* 4.7 8.3 - - - -
56D ASP* 3.5 25.4 + - - -
94D PRO* 4.1 9.5 - - - +
95D ILE* 1.3 82.7 - - - +
97D GLU* 1.3 59.1 + - - +
99D TYR* 3.7 7.9 - - - +
100D GLU* 3.2 29.7 + - - +
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Residues in contact with GLU 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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93D THR* 3.7 21.6 - - + +
94D PRO* 3.1 28.5 + - + +
95D ILE 3.1 0.4 - - - -
96D SER* 1.3 78.1 + - - +
98D VAL* 1.3 65.7 + - - +
99D TYR 3.1 1.6 - - - -
100D GLU* 3.4 18.7 - - - +
101D SER* 3.2 29.8 + - - -
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Residues in contact with VAL 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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60D MET* 3.9 16.2 - - + -
83D VAL* 4.2 21.5 - - + -
89D VAL* 3.9 21.1 - - + -
93D THR* 3.7 18.2 - - + -
94D PRO 3.1 14.7 + - - +
95D ILE* 3.2 10.5 + - + +
97D GLU* 1.3 75.1 - - - +
99D TYR* 1.3 54.3 + - - +
101D SER* 4.8 2.0 - - - -
102D GLU* 2.7 42.6 + - + +
103D LYS 3.9 0.2 + - - -
109D LEU* 3.9 22.4 - - + +
111D MET* 4.7 0.2 - - + -
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Residues in contact with TYR 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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20D VAL* 4.1 8.1 - - - +
24D ARG* 3.8 24.7 + - - -
31D ILE* 3.6 34.5 - - + -
32D PRO* 4.0 20.3 - - + +
95D ILE 2.8 17.0 + - - +
96D SER* 3.7 8.3 - - - +
98D VAL* 1.3 77.5 - - - +
100D GLU* 1.3 64.4 + - + +
103D LYS* 2.9 75.1 + - + +
107D GLY* 2.4 34.4 + - - -
109D LEU* 3.8 18.1 - - + +
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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 SER 3.2 12.6 + - - +
97D GLU* 3.4 24.0 - - - +
99D TYR* 1.3 82.3 - - + +
101D SER* 1.3 63.9 + - - +
103D LYS* 4.6 20.0 - - - +
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Residues in contact with SER 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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97D GLU* 3.2 20.2 + - - -
98D VAL* 4.2 2.5 - - - -
99D TYR 3.1 0.8 - - - -
100D GLU* 1.3 82.1 - - - +
102D GLU* 1.3 73.8 + - - +
103D LYS 3.7 1.0 - - - +
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Residues in contact with GLU 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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83D VAL* 3.7 24.2 - - + -
84D ASN* 3.0 39.0 + - - +
86D HIS* 5.6 1.9 + - - -
87D SER* 4.0 20.4 + - - +
89D VAL* 5.4 5.2 - - + -
98D VAL* 2.7 27.3 + - + +
101D SER* 1.3 87.8 + - - +
103D LYS* 1.3 68.0 + - - +
104D ASP* 3.6 1.2 + - - -
109D LEU* 3.8 7.7 - - + +
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Residues in contact with LYS 103 (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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98D VAL 3.9 0.6 + - - -
99D TYR* 2.9 68.9 + - + +
100D GLU* 4.6 16.7 - - - +
101D SER 3.7 0.9 - - - +
102D GLU* 1.3 80.3 - - - +
104D ASP* 1.3 69.3 + - - +
107D GLY* 4.4 10.1 - - - +
108D PHE 3.6 7.2 - - - +
109D LEU* 4.1 6.3 - - - +
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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