Contacts of the helix formed by residues 83 - 99 (chain A) in PDB entry 4II9
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 ASP 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 3.8 2.9 - - + +
80A ASP* 2.9 24.4 + - + +
81A VAL 4.0 1.6 - - - -
82A THR* 1.3 75.0 + - - +
84A VAL* 1.3 57.9 + - - +
85A ASP* 4.0 5.5 + - - +
86A LEU* 3.1 36.9 + - + +
87A LEU* 2.9 24.6 + - - +
402A GOL 4.5 1.9 + - - -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 3.7 3.8 - - - +
82A THR 3.1 14.1 + - - +
83A ASP* 1.3 72.3 + - - +
85A ASP* 1.3 59.0 + - - +
87A LEU* 3.9 8.3 - - + -
88A ASP* 2.9 34.1 + - - +
117A PHE* 3.7 27.1 - - + -
120A THR* 3.8 21.5 - - + -
121A LEU* 4.4 14.1 - - + -
124A HIS* 3.5 37.0 - - + +
126A TYR* 4.6 0.2 - - + -
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.3 5.8 + - - +
84A VAL* 1.3 78.1 - - - +
86A LEU* 1.3 61.2 + - - +
88A ASP* 3.4 8.6 + - - +
89A ARG* 3.3 28.2 + - - +
124A HIS* 3.3 22.2 - - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.7 15.9 - - + -
54A ILE* 3.9 20.0 - - + -
55A ALA* 4.8 2.7 - - + -
79A MET* 3.7 13.0 - - + -
83A ASP* 3.1 31.5 + - - +
85A ASP* 1.3 74.6 - - - +
87A LEU* 1.3 65.2 + - - +
89A ARG* 3.1 35.8 + - - +
90A LEU* 3.0 20.4 + - - +
402A GOL 3.5 34.3 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 5.1 0.4 - - + -
77A PRO* 3.7 30.3 - - + -
79A MET* 3.5 14.9 - - + +
81A VAL* 3.7 29.2 - - + +
83A ASP 2.9 12.4 + - - +
84A VAL* 3.3 11.9 + - + +
86A LEU* 1.3 74.9 - - - +
88A ASP* 1.3 65.4 + - - +
90A LEU* 3.0 3.8 + - + +
91A VAL* 2.8 34.6 + - + +
107A PHE* 3.8 22.7 - - + -
121A LEU* 3.9 24.0 - - + -
126A TYR* 4.0 14.4 - - + +
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 2.9 19.2 + - - +
85A ASP* 3.6 9.2 - - - +
86A LEU 3.2 0.2 - - - -
87A LEU* 1.3 77.4 - - - +
89A ARG* 1.3 57.7 + - + +
91A VAL* 3.4 0.7 + - - +
92A ASP* 2.8 42.2 + - - +
124A HIS* 2.6 34.8 + - - +
126A TYR* 2.7 42.9 + - - -
322A LYS* 5.7 2.6 + - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.8 29.9 - - + +
47A GLU 4.7 10.7 + - - -
54A ILE* 4.7 7.1 - - - +
85A ASP* 3.3 15.9 + - - +
86A LEU* 3.1 32.2 + - - +
88A ASP* 1.3 78.0 - - + +
90A LEU* 1.3 63.7 + - - +
92A ASP* 3.3 9.7 + - - +
93A GLU* 3.2 25.3 + - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.0 13.7 - - + +
45A TYR* 3.8 35.4 - - - -
46A LEU* 3.6 16.1 - - + +
55A ALA* 4.0 9.4 - - + +
56A ALA 4.0 5.8 - - - +
57A MET* 4.0 14.8 - - + -
77A PRO* 3.5 33.2 - - + -
79A MET* 3.7 18.6 - - - -
86A LEU 3.0 12.4 + - - +
87A LEU* 3.0 6.3 + - + +
89A ARG* 1.3 73.8 - - - +
91A VAL* 1.3 61.1 + - + +
93A GLU* 3.1 6.3 + - + +
94A ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 4.1 9.9 - - + -
87A LEU* 2.8 29.6 + - + +
88A ASP 3.8 2.2 - - - +
90A LEU* 1.3 75.1 - - - +
92A ASP* 1.4 60.4 + - - +
94A ALA* 3.1 6.8 + - - +
95A VAL* 2.8 30.6 + - + +
105A LEU* 4.3 5.4 - - + -
107A PHE* 3.9 23.3 - - + -
126A TYR* 3.7 19.7 - - + +
322A LYS* 3.8 43.5 - - + +
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 2.8 31.7 + - - +
89A ARG* 3.7 8.8 - - - +
90A LEU 3.2 0.2 - - - -
91A VAL* 1.4 77.3 - - - +
93A GLU* 1.3 61.6 + - - +
95A VAL* 3.4 6.9 + - - +
96A LYS* 3.1 43.1 + - - +
322A LYS* 4.2 17.8 + - - -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PRO* 3.1 29.8 - - - +
44A VAL* 3.8 17.4 - - + +
45A TYR 4.4 2.7 - - - +
46A LEU* 3.6 30.3 - - + -
89A ARG 3.2 9.2 + - - +
90A LEU* 3.1 11.2 + - + +
92A ASP* 1.3 76.1 - - - +
94A ALA* 1.4 62.9 + - - +
96A LYS* 2.7 41.4 + - - +
97A ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.7 16.1 - - + +
57A MET* 4.0 6.7 - - - -
59A MET* 3.8 17.6 - - + +
90A LEU 2.9 13.3 + - - +
91A VAL* 3.4 8.5 - - - +
93A GLU* 1.4 77.1 - - - +
95A VAL* 1.4 57.1 + - - +
97A ALA* 3.1 4.9 + - - +
98A LEU* 2.9 34.7 + - - +
105A LEU* 3.5 24.7 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 2.8 26.3 + - + +
92A ASP* 3.8 7.4 - - - +
94A ALA* 1.4 71.1 - - - +
96A LYS* 1.3 62.5 + - + +
98A LEU* 3.2 9.3 + - - +
99A ASP* 3.2 17.5 + - - -
100A GLY 4.7 1.4 + - - -
105A LEU* 4.7 5.8 - - + -
322A LYS* 4.1 20.9 - - + -
324A LEU* 3.7 39.5 - - + -
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Residues in contact with LYS 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 ASP* 3.1 32.7 + - - +
93A GLU* 2.7 37.5 + - - +
95A VAL* 1.3 75.3 - - + +
97A ALA* 1.3 62.1 + - - +
99A ASP* 3.2 18.8 + - - +
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Residues in contact with ALA 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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2A VAL* 4.0 15.0 - - + -
42A VAL* 3.7 23.7 - - + +
44A VAL* 3.6 28.9 - - + -
93A GLU 3.1 6.7 + - - +
94A ALA 3.1 8.3 + - - +
96A LYS* 1.3 74.3 - - - +
98A LEU* 1.3 64.8 + - - +
99A ASP* 3.4 5.4 + - - +
101A ARG* 5.5 2.9 + - - -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.6 4.7 - - + -
59A MET* 4.0 22.4 - - + -
61A LEU* 3.8 39.0 - - + -
71A ALA* 3.8 21.8 - - + -
94A ALA 2.9 22.8 + - - +
95A VAL* 3.2 8.0 + - - +
97A ALA* 1.3 75.6 - - - +
99A ASP* 1.4 69.8 + - - +
100A GLY 4.7 2.7 - - - +
101A ARG* 3.1 28.2 + - - +
102A ALA* 4.3 11.0 - - + +
105A LEU* 4.1 8.7 - - + -
324A LEU* 4.0 25.6 - - + -
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Residues in contact with ASP 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 VAL 3.2 6.9 + - - -
96A LYS 3.2 16.5 + - - +
97A ALA 3.2 7.2 - - - +
98A LEU* 1.4 78.4 - - - +
100A GLY* 1.3 59.7 + - - +
101A ARG* 3.2 14.0 + - - +
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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
------------------------------------------------------------
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