Contacts of the helix formed by residues 85 - 95 (chain B) in PDB entry 4XZC
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 CYS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.4 26.2 - - + +
7B ALA* 3.8 21.1 - - + +
8B ASN 5.6 1.1 - - - -
13B TYR* 3.9 11.0 - - + -
81B GLY 2.9 11.4 + - - +
82B TRP* 3.1 36.0 + - - -
84B CYS* 1.3 80.5 - - - +
86B THR* 1.3 60.2 + - - +
88B MET* 3.0 17.4 + - - -
89B VAL* 2.9 25.3 + - - +
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Residues in contact with THR 86 (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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3B ASN* 3.5 43.5 - - + +
5B ILE 2.9 11.0 + - - +
6B LYS* 3.3 8.5 - - + +
7B ALA 3.0 25.6 + - - -
8B ASN* 4.8 2.8 + - - -
85B CYS* 1.3 71.3 - - - +
87B GLY* 1.3 56.7 + - - +
89B VAL* 3.3 3.5 + - - +
90B GLU* 2.9 32.8 + - - +
322B PRO* 5.2 7.1 - - + +
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Residues in contact with GLY 87 (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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7B ALA 2.8 24.0 + - - -
8B ASN* 4.0 21.5 + - - -
85B CYS* 4.7 0.4 - - - -
86B THR* 1.3 73.0 + - - +
88B MET* 1.3 51.5 + - - +
90B GLU* 3.4 5.6 + - - +
91B ASN* 2.7 47.6 + - - +
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Residues in contact with MET 88 (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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82B TRP* 3.4 63.5 - - + +
83B ALA* 3.8 8.1 - - - +
85B CYS* 3.0 16.9 + - - +
87B GLY* 1.3 74.1 - - - +
89B VAL* 1.3 61.2 + - - +
91B ASN* 4.4 2.9 - - + +
92B GLY* 2.9 21.7 + - - +
133B TRP* 4.2 8.3 - - - -
137B ASN* 3.5 36.6 - - - +
139B PHE* 4.0 15.9 - - + -
312B TYR* 3.1 23.1 + - + +
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Residues in contact with VAL 89 (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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3B ASN* 3.9 5.8 - - - +
84B CYS 3.1 28.3 - - - +
85B CYS 2.9 9.9 + - - +
86B THR* 3.8 5.2 - - - +
88B MET* 1.3 77.5 - - - +
90B GLU* 1.3 62.0 + - - +
93B LEU* 3.1 43.2 + - + +
312B TYR* 3.4 15.0 - - - +
322B PRO* 4.0 12.6 - - + -
325B PHE* 3.4 54.3 - - + -
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Residues in contact with GLU 90 (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 THR 2.9 17.5 + - - +
87B GLY* 3.6 6.7 - - - +
89B VAL* 1.3 80.4 - - - +
91B ASN* 1.3 65.5 + - - +
93B LEU* 4.0 1.6 - - - +
94B LYS* 3.1 57.4 + - + +
322B PRO* 4.0 27.6 - - + +
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Residues in contact with ASN 91 (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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8B ASN 5.4 4.6 + - - -
87B GLY* 2.7 27.0 + - - +
88B MET* 4.6 3.5 - - + +
90B GLU* 1.3 74.7 - - - +
92B GLY* 1.3 62.4 + - - +
94B LYS* 3.7 19.8 + - - -
95B TRP* 3.1 29.1 + - - +
98B LYS* 4.9 6.5 + - - +
137B ASN* 3.2 28.4 + - + +
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Residues in contact with GLY 92 (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 MET 2.9 20.5 + - - -
91B ASN* 1.3 78.1 - - - +
93B LEU* 1.3 58.6 + - - +
95B TRP* 4.1 0.5 - - - +
96B PHE* 3.3 15.9 - - - -
133B TRP* 3.2 38.4 + - - -
137B ASN* 3.8 5.7 + - - -
312B TYR* 3.9 10.2 - - - +
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Residues in contact with LEU 93 (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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89B VAL* 3.1 31.3 + - + +
90B GLU* 4.0 2.0 - - - +
91B ASN 3.2 0.6 - - - -
92B GLY* 1.3 80.0 - - - +
94B LYS* 1.3 63.5 + - + +
95B TRP 3.4 0.2 - - - -
96B PHE* 3.5 4.7 + - - +
312B TYR* 4.1 12.3 - - + +
315B ALA* 3.8 14.4 - - + -
316B TRP* 3.0 65.5 - - + +
320B ILE* 3.3 37.7 - - + +
321B THR* 3.8 15.5 - - - -
322B PRO* 4.0 4.9 - - + -
325B PHE* 5.7 0.4 - - + -
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Residues in contact with LYS 94 (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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90B GLU* 3.1 42.0 + - + +
91B ASN* 3.7 23.2 + - - +
93B LEU* 1.3 76.3 - - + +
95B TRP* 1.3 60.2 + - - +
96B PHE 2.9 2.0 - - - -
97B ASP* 2.7 38.0 + - + +
98B LYS* 3.1 32.6 + - + +
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Residues in contact with TRP 95 (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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91B ASN 3.1 21.6 + - - +
92B GLY 4.1 4.7 - - - +
94B LYS* 1.3 76.5 - - - +
96B PHE* 1.3 102.5 + + - +
98B LYS* 3.0 26.9 + - - +
99B ASN* 3.1 52.2 + - + +
102B VAL* 4.7 2.9 - - + -
103B ILE* 3.8 19.1 - - + -
129B ALA* 3.8 16.6 - - + -
132B LYS* 4.0 9.0 - - + -
133B TRP* 3.3 36.8 - + + +
136B ASP* 2.6 38.2 + - + -
137B ASN* 3.8 15.0 - - - +
309B PHE* 4.3 2.2 - + - -
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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