Contacts of the helix formed by residues 95 - 105 (chain B) in PDB entry 5C5A
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 GLU 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.6 8.9 - - + -
92B SER* 2.9 45.8 + - - +
93B VAL 3.2 0.4 - - - -
94B LYS* 1.3 77.5 - - + +
96B HIS* 1.3 58.8 + - - +
97B ARG 3.4 2.7 - - - -
98B LYS* 2.8 44.6 + - + -
99B ILE* 3.0 31.0 + - + +
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Residues in contact with HIS 96 (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 VAL 3.0 28.3 + - - -
94B LYS* 2.9 16.6 + - - +
95B GLU* 1.3 72.7 - - - +
97B ARG* 1.3 61.7 + - - +
99B ILE* 3.3 0.5 + - - -
100B TYR* 2.9 37.5 + - + -
201B NUT 3.4 47.3 + + + +
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Residues in contact with ARG 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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95B GLU 3.4 0.4 - - - -
96B HIS* 1.3 76.8 - - - +
98B LYS* 1.3 58.8 + - - +
100B TYR* 3.5 3.9 + - - +
101B THR* 2.9 51.1 + - + +
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Residues in contact with LYS 98 (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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88B VAL* 5.1 17.5 - - + +
90B SER 5.1 5.0 + - - +
91B PHE* 4.2 15.9 - - + +
95B GLU* 2.8 49.1 + - + +
97B ARG* 1.3 79.5 - - - +
99B ILE* 1.3 58.2 + - + +
101B THR* 3.2 7.1 + - - -
102B MET* 2.9 51.8 + - + +
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Residues in contact with ILE 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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54B LEU* 4.2 2.2 - - + -
86B PHE* 4.5 7.1 - - + -
91B PHE* 3.8 29.6 - - + -
92B SER 3.7 19.3 - - - +
93B VAL* 3.9 8.5 - - - +
95B GLU* 3.0 20.9 + - + +
96B HIS 3.9 3.4 - - - +
98B LYS* 1.3 75.2 - - + +
100B TYR* 1.3 66.5 + - - +
102B MET* 3.9 3.9 - - - +
103B ILE* 2.9 46.7 + - + +
201B NUT 3.7 54.1 - - + -
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Residues in contact with TYR 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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50B MET* 4.1 27.1 - - + +
54B LEU* 3.6 20.2 - - + +
96B HIS* 2.9 33.3 + - + +
97B ARG* 4.0 4.5 - - - +
99B ILE* 1.3 76.5 - - - +
101B THR* 1.3 61.2 + - + +
103B ILE* 3.2 6.5 + - - +
104B TYR* 2.9 59.3 + + + -
201B NUT 3.4 25.8 - + + -
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Residues in contact with THR 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 ARG* 2.9 51.9 + - + +
98B LYS* 3.2 10.2 + - - -
100B TYR* 1.3 74.4 - - + +
102B MET* 1.3 78.6 + - - +
104B TYR* 3.3 10.3 + - + +
105B ARG* 3.0 31.3 + - - +
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Residues in contact with MET 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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86B PHE* 3.3 54.5 - - + +
88B VAL* 5.0 9.6 - - + -
98B LYS* 2.9 34.3 + - + +
99B ILE 4.0 2.7 - - - +
101B THR* 1.3 96.1 + - - +
103B ILE* 1.3 66.9 + - - +
105B ARG* 3.1 51.5 + - - +
106B ASN* 2.9 23.8 + - - +
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Residues in contact with ILE 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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34B LEU* 4.8 3.3 - - + +
50B MET* 3.8 18.2 - - - -
53B VAL* 4.1 10.8 - - + -
54B LEU* 3.4 35.4 - - + -
57B LEU* 3.5 28.0 - - + -
86B PHE* 3.8 12.8 - - + -
99B ILE* 2.9 30.4 + - + +
100B TYR* 3.6 5.4 - - - +
102B MET* 1.3 75.9 - - - +
104B TYR* 1.3 59.1 + - - +
106B ASN* 2.8 24.1 + - - +
107B LEU* 3.4 28.9 - - + +
201B NUT 5.1 0.2 - - + -
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Residues in contact with TYR 104 (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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56A TYR* 5.4 0.3 + - - -
26B THR* 4.4 13.0 + - + +
50B MET* 3.7 22.0 - - + +
100B TYR* 2.9 54.1 + + + +
101B THR* 3.8 9.2 - - + +
102B MET 3.3 0.2 - - - -
103B ILE* 1.3 76.0 - - - +
105B ARG* 1.3 56.9 + - - +
106B ASN 3.1 0.2 + - - -
107B LEU* 3.0 43.5 - - + +
109B VAL* 3.7 24.7 - - + -
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Residues in contact with ARG 105 (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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43A ALA* 4.0 26.8 - - + +
56A TYR* 3.5 5.6 + - - -
31B LYS* 3.0 23.7 + - - -
101B THR* 3.0 21.6 + - - +
102B MET* 3.1 45.7 + - - +
104B TYR* 1.3 74.1 - - + +
106B ASN* 1.3 63.5 + - - +
107B LEU 3.6 0.9 - - - -
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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