Contacts of the helix formed by residues 81 - 92 (chain A) in PDB entry 4B92
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.8 4.8 - - - +
70A HIS* 4.0 27.1 - - + +
79A VAL 3.7 4.0 + - - -
80A ASP* 1.3 76.7 - - - +
82A PHE* 1.3 60.2 + - - +
83A TYR* 3.6 8.1 - - - +
84A HIS* 2.7 48.5 + - - +
85A GLY* 2.9 25.5 + - - -
123A LYS* 3.8 25.6 + - + +
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Residues in contact with PHE 82 (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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69A PHE* 3.5 46.7 - + + -
70A HIS* 4.0 16.5 - + + +
81A ASP* 1.3 76.2 - - - +
83A TYR* 1.3 51.9 + - - +
85A GLY 4.0 0.2 - - - -
86A THR* 2.8 38.8 + - - +
97A ILE* 4.3 13.0 - - + -
99A GLY* 5.1 5.2 - - - -
100A HIS 5.9 1.1 - - - -
116A CYS* 4.0 25.4 - - - -
119A LEU* 3.8 18.1 + - + +
120A ALA* 3.5 43.5 - - + -
123A LYS* 4.2 6.7 - - + +
124A VAL* 3.9 15.2 - - + -
128A TYR* 4.7 5.6 - + - -
130A LEU* 4.7 6.5 - - + -
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Residues in contact with TYR 83 (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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81A ASP* 3.1 13.2 + - - +
82A PHE* 1.3 76.1 - - - +
84A HIS* 1.3 92.1 + + - +
86A THR* 3.1 3.4 + - - -
87A LYS* 2.9 45.2 + - + +
123A LYS* 3.5 40.3 + - + +
125A CYS* 3.5 22.4 - - - -
452A PHE* 3.8 20.2 - + - -
454A CYS 3.8 13.5 + - - -
456A GLU* 3.8 27.8 - - + -
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Residues in contact with HIS 84 (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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79A VAL 5.9 1.1 - - - -
80A ASP* 3.9 19.5 - - - +
81A ASP* 2.7 39.1 + - - +
83A TYR* 1.3 97.3 - + - +
85A GLY* 1.3 57.3 - - - +
87A LYS* 3.5 15.4 + - - +
88A ALA* 2.8 30.7 + - - +
419A VAL 4.4 11.9 + - - +
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Residues in contact with GLY 85 (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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69A PHE* 3.3 38.4 - - - -
80A ASP* 4.0 6.7 - - - +
81A ASP 2.9 15.7 + - - -
84A HIS* 1.3 76.8 - - - +
86A THR* 1.3 59.4 + - - +
88A ALA* 3.2 7.3 + - - +
89A ALA* 2.9 24.3 + - - +
351A VAL* 4.1 0.9 - - - +
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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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69A PHE* 4.2 4.9 - - + -
82A PHE 2.8 24.2 + - - +
83A TYR 3.1 7.8 + - - -
85A GLY* 1.3 71.1 - - - +
87A LYS* 1.3 65.6 + - - +
89A ALA* 3.1 9.8 + - - +
90A LEU* 3.0 27.7 + - - +
97A ILE* 4.0 15.7 - - + -
124A VAL* 3.8 15.9 - - + -
125A CYS* 2.9 32.1 + - - +
126A CYS* 3.7 24.0 - - - +
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Residues in contact with LYS 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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83A TYR* 2.9 36.3 + - + +
84A HIS* 3.5 15.7 + - - +
86A THR* 1.3 77.9 + - - +
88A ALA* 1.3 63.5 + - - +
90A LEU* 3.1 4.2 + - - +
91A VAL* 3.1 26.8 + - + +
125A CYS* 4.4 2.4 - - - +
419A VAL* 4.6 24.7 - - + +
452A PHE* 3.6 59.1 - - + +
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Residues in contact with ALA 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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80A ASP* 4.9 0.2 - - - +
84A HIS 2.8 18.5 + - - +
85A GLY* 3.4 7.2 - - - +
87A LYS* 1.3 75.9 - - - +
89A ALA* 1.3 63.1 + - - +
91A VAL* 3.7 0.7 + - - +
92A GLY 3.2 14.7 + - - -
351A VAL* 3.4 20.6 - - + -
352A GLN* 3.3 16.1 - - + +
419A VAL* 3.7 15.3 - - + -
420A GLN* 3.9 24.7 - - + -
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Residues in contact with ALA 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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85A GLY 2.9 12.6 + - - +
86A THR* 3.2 11.0 - - - +
88A ALA* 1.3 76.7 - - - +
90A LEU* 1.3 54.2 + - + +
92A GLY* 2.8 22.0 + - - -
93A GLY 3.0 0.5 + - - -
94A THR* 2.9 48.5 + - + +
97A ILE* 4.0 12.1 - - + -
126A CYS* 4.8 0.9 - - - -
351A VAL* 3.9 19.5 - - + +
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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
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86A THR 3.0 19.6 + - - +
87A LYS 3.1 4.7 + - - +
89A ALA* 1.3 77.7 - - - +
91A VAL* 1.3 60.5 + - - +
93A GLY 3.0 6.1 + - - -
94A THR 3.3 16.4 - - - +
95A THR* 3.9 6.1 - - - -
125A CYS* 3.5 36.1 - - + +
126A CYS* 3.7 17.0 - - + -
439A THR* 2.7 45.6 + - + -
441A SER* 4.0 7.4 - - - -
446A VAL* 3.9 21.8 - - + -
447A TYR* 4.8 1.1 - - - -
452A PHE* 3.8 22.0 - - + -
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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
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87A LYS* 3.1 18.5 + - + +
88A ALA 4.1 4.5 - - - +
90A LEU* 1.3 74.8 - - - +
92A GLY* 1.3 57.3 + - - +
352A GLN* 3.6 21.4 + - - +
411A LYS* 6.0 2.2 - - - +
419A VAL* 4.2 20.4 - - + -
436A PRO* 3.3 19.1 - - - +
447A TYR* 3.6 50.3 + - + +
452A PHE* 3.9 19.7 - - + -
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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 ALA 3.2 9.4 + - - -
89A ALA 2.8 12.0 + - - -
91A VAL* 1.3 78.6 - - - +
93A GLY* 1.3 55.7 + - - -
94A THR* 3.4 1.5 + - - -
351A VAL 5.1 1.0 - - - +
352A GLN* 3.5 29.8 - - - +
355A MET* 3.3 27.5 - - - +
356A SER* 4.9 1.0 + - - -
405A TRP* 4.5 0.5 - - - -
436A PRO* 3.9 9.4 - - - +
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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