Contacts of the helix formed by residues 85 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.4 25.6 - - + +
7A ALA* 3.7 20.9 - - + -
8A ASN 6.0 0.4 - - - -
13A TYR* 3.9 9.9 - - + -
81A GLY 2.8 11.2 + - - +
82A TRP* 3.7 35.0 - - - -
83A ALA 3.6 0.6 - - - -
84A CYS* 1.3 80.5 - - - +
86A THR* 1.3 60.2 + - - +
87A GLY* 4.6 0.2 - - - -
88A MET* 3.1 16.5 + - - +
89A VAL* 2.9 24.8 + - - +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASN* 3.6 39.9 - - + +
5A ILE 2.9 16.0 + - - +
6A LYS* 3.3 10.5 - - + +
7A ALA 2.8 27.0 + - - -
8A ASN* 4.6 6.0 + - - -
85A CYS* 1.3 73.1 - - - +
87A GLY* 1.3 60.0 + - - +
89A VAL* 3.8 2.9 - - - +
90A GLU* 3.2 31.4 + - - +
322A PRO* 5.6 1.4 - - - +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA 2.8 23.6 + - - -
8A ASN* 3.9 22.4 - - - -
85A CYS* 3.3 0.9 - - - -
86A THR* 1.3 69.6 + - - +
88A MET* 1.3 61.1 + - - +
90A GLU* 3.4 4.1 + - - +
91A ASN* 2.8 43.5 + - - +
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TRP* 3.3 64.2 - - + +
83A ALA* 3.4 11.9 - - - +
85A CYS* 3.1 14.9 + - - +
87A GLY* 1.3 77.4 - - - +
89A VAL* 1.3 54.9 + - - +
91A ASN* 4.9 0.9 - - - -
92A GLY* 2.7 33.2 + - - +
133A TRP* 4.3 11.4 - - - -
137A ASN* 4.1 25.8 - - - +
139A PHE* 3.6 20.4 - - + -
312A TYR* 3.3 22.5 + - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASN* 3.8 7.4 - - - +
84A CYS 3.5 25.1 - - - +
85A CYS 2.9 9.3 + - - +
86A THR* 4.0 4.5 - - - +
87A GLY 3.3 0.2 - - - -
88A MET* 1.3 74.6 - - - +
90A GLU* 1.3 64.4 + - - +
93A LEU* 3.2 33.2 + - + +
312A TYR* 3.3 17.0 - - - +
322A PRO* 3.7 31.2 - - + -
325A PHE* 3.6 42.8 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 4.6 9.9 - - - +
86A THR* 3.2 19.7 + - - +
87A GLY* 3.7 4.3 - - - +
89A VAL* 1.3 80.2 - - - +
91A ASN* 1.3 60.3 + - - +
93A LEU* 4.3 1.0 - - - +
94A LYS* 3.2 49.9 + - - +
322A PRO* 3.9 25.8 - - + +
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Residues in contact with ASN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 5.8 2.4 + - - -
87A GLY* 2.8 27.8 + - - +
88A MET* 4.3 2.0 - - - +
90A GLU* 1.3 75.0 - - - +
92A GLY* 1.3 57.3 + - - +
93A LEU 3.1 1.8 - - - -
94A LYS* 3.6 21.3 + - + +
95A TRP* 2.8 36.6 + - - +
137A ASN* 3.5 21.1 + - + +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MET* 2.7 23.7 + - - +
91A ASN* 1.3 72.7 - - - +
93A LEU* 1.3 56.1 + - - +
95A TRP* 3.8 1.2 - - - +
96A PHE* 3.2 18.9 - - - -
133A TRP* 3.1 44.2 + - - -
137A ASN* 3.8 5.1 + - - +
312A TYR* 3.6 8.5 - - - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.2 29.0 + - + +
90A GLU* 4.3 1.6 - - - +
91A ASN 3.1 0.8 - - - -
92A GLY* 1.3 76.4 - - - +
94A LYS* 1.3 65.0 + - - +
95A TRP 3.3 0.7 + - - -
96A PHE* 3.3 7.6 + - - -
97A ASP* 4.8 0.2 - - - -
312A TYR* 3.7 18.4 - - + +
315A ALA* 3.7 12.1 - - + -
316A TRP* 3.2 62.7 - - + +
320A ILE* 3.3 38.6 - - + +
321A THR* 4.2 11.7 - - - -
322A PRO* 4.3 4.3 - - + -
325A PHE* 5.0 1.8 - - + -
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLU* 3.2 41.7 + - - +
91A ASN* 3.6 21.2 + - + +
93A LEU* 1.3 75.0 - - - +
95A TRP* 1.3 68.6 + - - +
96A PHE 3.0 2.7 - - - -
97A ASP* 2.9 27.1 + - + +
98A LYS* 3.3 28.9 + - + +
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Residues in contact with TRP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASN 2.8 23.5 + - - +
92A GLY 3.8 6.5 - - - +
93A LEU 3.2 0.2 - - - -
94A LYS* 1.3 72.7 - - - +
96A PHE* 1.3 94.2 + + - +
98A LYS* 3.3 12.8 + - + -
99A ASN* 2.9 62.5 + - + +
102A VAL* 4.3 5.4 - - + -
103A ILE* 4.0 16.8 - - + -
129A ALA 3.7 16.8 - - - -
132A LYS* 4.0 10.3 - - + -
133A TRP* 3.3 34.8 - + - +
136A ASP* 2.9 42.5 + - + +
137A ASN* 3.6 16.6 - - - +
309A PHE* 3.7 9.2 - + - -
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 3.2 29.2 - - - -
93A LEU 3.6 4.9 - - - -
94A LYS 3.0 1.4 + - - -
95A TRP* 1.3 101.2 - + - +
97A ASP* 1.3 60.4 + - - +
99A ASN* 3.2 11.4 + - - +
100A LYS* 3.4 18.7 + - - +
103A ILE* 4.1 14.2 - - + +
133A TRP* 3.7 7.4 - - - -
309A PHE* 3.6 29.6 - + - -
312A TYR* 3.7 4.5 - - + -
313A TYR* 3.4 56.8 - + + -
316A TRP* 3.3 36.3 - + + +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS* 2.9 21.8 + - + +
96A PHE* 1.3 76.2 - - - +
98A LYS* 1.3 61.3 + - + +
100A LYS* 3.9 14.5 - - - +
316A TRP* 3.2 33.4 + - - -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS* 3.9 28.5 - - + +
95A TRP* 3.3 13.6 + - + +
96A PHE 3.2 0.6 - - - -
97A ASP* 1.3 77.4 - - + +
99A ASN* 1.3 72.6 + - - +
100A LYS 3.5 2.7 + - - -
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TRP* 2.9 66.7 + - + +
96A PHE 3.2 5.5 + - - +
98A LYS* 1.3 90.7 - - - +
100A LYS* 1.3 63.2 + - - +
101A ASP* 3.0 5.6 + - - +
102A VAL* 3.2 19.7 + - + +
103A ILE* 3.4 14.6 + - - +
132A LYS* 2.8 34.4 + - - +
136A ASP* 4.3 1.0 + - - -
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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