Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 3CZ9
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 SER 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.5 17.4 - - - +
81A ASN 3.4 12.7 + - - -
82A LEU 3.3 2.4 + - - -
83A SER 3.3 0.2 - - - -
84A GLU* 1.3 77.2 - - - +
86A ALA* 1.3 63.9 + - - +
87A ALA* 3.2 9.0 + - - +
88A VAL* 3.0 35.7 + - - +
89A LYS* 3.0 17.2 + - - -
115A HIS* 3.3 11.0 + - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU 3.6 4.9 + - - -
85A SER* 1.3 72.1 - - - +
87A ALA* 1.3 61.8 + - - +
89A LYS* 3.3 15.6 + - + +
90A GLU* 3.0 23.2 + - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.3 0.9 - - + -
58A LEU* 4.1 17.5 - - + -
62A LYS* 5.1 2.6 - - + -
85A SER* 3.2 8.4 + - - +
86A ALA* 1.3 78.8 - - - +
88A VAL* 1.3 62.7 + - - +
90A GLU* 3.3 13.0 + - - +
91A ILE* 3.0 30.9 + - + +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.3 12.8 - - + -
38A LEU* 3.6 21.3 - - + -
58A LEU* 4.1 8.1 - - + -
72A LEU* 4.8 4.0 - - + -
82A LEU* 3.6 42.4 - - + +
85A SER* 3.0 19.2 + - - +
87A ALA* 1.3 74.6 - - - +
89A LYS* 1.3 66.3 + - - +
91A ILE* 3.2 6.9 + - - +
92A LEU* 2.9 45.5 + - + +
115A HIS* 3.8 3.6 - - + +
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Residues in contact with LYS 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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83A SER 5.0 1.2 + - - -
85A SER 3.0 8.5 + - - +
86A ALA* 3.4 17.3 - - + +
87A ALA 3.3 0.2 - - - -
88A VAL* 1.3 76.4 - - - +
90A GLU* 1.3 58.9 + - - +
92A LEU* 3.8 1.4 - - - +
93A LYS* 2.9 63.2 + - + +
114A ALA 3.7 14.1 + - - -
115A HIS* 2.7 51.8 + - + +
117A ILE* 5.0 0.2 - - - +
500A P4C 6.2 1.6 - - - -
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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
----------------------------------------------------------
62A LYS* 3.1 33.6 + - - +
86A ALA 3.0 13.4 + - - +
87A ALA* 3.6 12.2 - - - +
89A LYS* 1.3 77.8 - - - +
91A ILE* 1.3 62.0 + - - +
93A LYS* 3.8 5.4 - - - +
94A GLU* 2.9 47.9 + - + +
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Residues in contact with ILE 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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7A LEU* 4.2 10.8 - - + -
9A ILE* 4.4 5.2 - - + -
58A LEU* 3.5 41.1 - - + -
62A LYS* 3.8 34.3 - - + -
70A VAL* 4.1 33.9 - - + -
87A ALA* 3.0 23.0 + - + +
88A VAL* 3.2 4.7 + - - +
90A GLU* 1.3 77.0 - - - +
92A LEU* 1.3 58.1 + - + +
94A GLU* 3.4 8.0 + - - +
95A GLN* 2.9 26.5 + - - +
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Residues in contact with LEU 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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70A VAL* 3.9 27.1 - - + -
72A LEU* 4.1 21.5 - - + -
88A VAL* 2.9 38.9 + - + +
89A LYS 3.9 1.8 - - - +
91A ILE* 1.3 73.9 - - + +
93A LYS* 1.3 62.0 + - - +
95A GLN* 3.2 3.2 + - - +
96A GLU* 2.9 31.4 + - - +
102A ILE* 3.8 30.2 - - + +
111A ALA 4.6 1.3 - - - +
112A LEU* 4.3 5.2 - - + -
115A HIS* 3.9 16.4 - - + -
117A ILE* 3.7 25.1 - - + +
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Residues in contact with LYS 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 LYS* 2.9 43.8 + - + +
90A GLU* 3.9 5.4 - - - +
92A LEU* 1.3 75.6 - - - +
94A GLU* 1.3 59.8 + - + +
96A GLU* 3.4 10.0 + - - +
97A ASN* 2.8 29.8 + - - +
115A HIS 3.3 23.9 + - - -
116A GLU* 4.4 16.4 + - - +
117A ILE* 4.0 12.4 - - + +
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Residues in contact with GLU 94 (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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62A LYS* 3.6 25.3 + - - +
90A GLU* 2.9 40.8 + - + +
91A ILE* 3.8 5.7 - - - +
93A LYS* 1.3 77.1 - - + +
95A GLN* 1.4 62.0 + - - +
97A ASN* 3.2 7.2 + - - +
98A ARG* 3.0 29.8 + - - +
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Residues in contact with GLN 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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66A PRO* 4.9 1.0 - - - +
67A TYR 3.0 25.2 + - - +
68A ASP 3.7 4.6 + - - -
69A VAL* 3.9 3.2 - - - +
70A VAL* 3.9 18.3 - - + +
91A ILE 2.9 18.9 + - - +
92A LEU* 3.7 5.2 - - - +
94A GLU* 1.4 72.9 - - - +
96A GLU* 1.3 67.0 + - - +
98A ARG* 3.3 23.6 + - - +
99A LYS 3.2 3.5 + - - -
100A GLY* 2.9 53.5 + - - +
101A LEU 3.0 19.5 + - - +
102A ILE* 3.6 18.2 - - + -
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Residues in contact with GLU 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 LEU 2.9 16.4 + - - +
93A LYS* 3.7 10.5 + - - +
95A GLN* 1.3 76.7 - - - +
97A ASN* 1.3 65.5 + - - +
99A LYS* 3.1 15.3 + - - +
100A GLY 4.8 3.6 - - - -
102A ILE* 4.2 11.3 - - + +
116A GLU 4.5 4.7 - - - +
117A ILE* 3.7 20.1 - - + +
118A GLY* 2.9 33.2 + - - -
152A ILE* 6.0 2.5 - - + -
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Residues in contact with ASN 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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93A LYS 2.8 18.4 + - - +
94A GLU* 3.2 8.7 + - - +
96A GLU* 1.3 80.4 - - - +
98A ARG* 1.3 58.2 + - - +
99A LYS* 3.2 14.6 + - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 3.5 37.7 - - - +
67A TYR 2.9 29.3 + - - -
68A ASP* 4.7 7.7 + - - +
94A GLU* 3.0 21.6 + - - +
95A GLN* 3.3 27.6 + - - +
97A ASN* 1.3 75.2 - - - +
99A LYS* 1.3 68.6 + - - +
100A GLY* 4.0 7.4 - - - +
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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