Contacts of the helix formed by residues 94 - 103 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP 3.6 14.4 - - - +
57B HIS* 4.2 13.5 - - - +
58B VAL 3.8 6.3 - - - +
59B ASN* 4.3 2.7 - - + -
92B SER 3.5 7.1 - - - +
93B THR* 1.3 92.0 - - + +
95B ILE* 1.3 62.4 + - - +
96B SER* 4.0 9.0 - - - +
97B GLU* 2.9 40.4 + - + +
98B VAL* 3.1 7.8 + - - +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.9 15.0 - - + -
33B VAL* 3.6 30.1 - - + -
54B VAL* 3.7 22.7 - - + -
55B PRO 3.1 27.4 - - - +
56B ASP 3.5 1.1 + - - +
58B VAL 2.8 20.4 + - - +
59B ASN* 5.1 3.1 - - - -
60B MET* 5.3 3.8 - - - +
63B LEU* 4.4 5.8 - - + -
93B THR 3.4 1.5 + - - -
94B PRO* 1.3 71.9 - - - +
96B SER* 1.3 59.6 + - - +
98B VAL* 3.7 10.5 - - + -
99B TYR* 2.8 29.5 + - - +
109B LEU* 3.9 14.1 - - + -
111B MET* 3.9 18.2 - - + -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.9 16.1 - - - +
56B ASP* 3.2 39.3 + - - +
94B PRO* 4.0 8.1 - - - +
95B ILE* 1.3 79.0 - - - +
97B GLU* 1.3 65.7 + - - +
99B TYR* 3.6 3.8 - - - +
100B GLU* 3.2 26.0 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 3.6 17.3 - - + +
94B PRO* 2.9 31.6 + - + +
96B SER* 1.3 83.1 + - - +
98B VAL* 1.3 65.0 + - - +
100B GLU* 3.3 8.0 + - - +
101B SER* 3.3 22.3 + - - -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B MET* 4.7 8.1 - - + -
83B VAL* 4.3 18.2 - - + -
89B VAL* 4.4 21.8 - - + -
93B THR* 3.8 26.2 - - + +
94B PRO 3.1 12.8 + - - +
95B ILE* 3.2 12.3 + - + +
97B GLU* 1.3 74.6 - - - +
99B TYR* 1.3 58.0 + - - +
101B SER* 3.3 6.2 + - - -
102B GLU* 2.8 45.2 + - + +
109B LEU* 4.1 17.5 - - + -
111B MET* 5.4 0.7 - - + -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 4.0 10.7 - - - +
24B ARG* 4.1 27.4 + - - +
31B ILE* 3.5 35.9 - - + -
32B PRO* 4.1 16.1 - - + +
95B ILE 2.8 20.4 + - - +
96B SER 3.6 6.5 - - - +
97B GLU 3.2 0.2 - - - -
98B VAL* 1.3 73.8 - - - +
100B GLU* 1.3 77.6 + - - +
103B LYS* 3.0 61.9 + - + +
107B GLY* 2.6 34.8 + - - -
109B LEU* 4.0 18.6 - - + +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 5.3 3.5 + - - -
96B SER 3.2 14.3 + - - +
97B GLU* 3.3 11.4 + - - +
99B TYR* 1.3 99.1 - - - +
101B SER* 1.3 58.8 + - - +
103B LYS* 4.3 22.8 + - - +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU 3.3 13.8 + - - -
98B VAL* 3.3 6.8 + - - -
99B TYR 3.2 0.4 - - - -
100B GLU* 1.3 80.9 - - - +
102B GLU* 1.3 79.4 + - - +
103B LYS 3.8 0.2 - - - -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.7 21.8 - - + -
84B ASN* 3.1 40.7 + - - +
89B VAL* 5.2 13.3 - - + +
98B VAL* 2.8 32.1 + - + +
101B SER* 1.3 92.9 + - - +
103B LYS* 1.3 68.4 + - - +
104B ASP 3.6 0.5 + - - -
109B LEU* 3.8 9.9 - - + +
110B TYR 5.4 0.5 + - - -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 5.2 0.7 + - - -
99B TYR* 3.0 59.1 + - + +
100B GLU* 4.3 26.5 + - - +
101B SER 3.8 0.4 - - - -
102B GLU* 1.3 80.4 - - - +
104B ASP* 1.3 72.4 + - - +
107B GLY* 4.6 5.4 - - - +
108B PHE 3.7 6.3 - - - +
109B LEU* 4.2 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