Contacts of the helix formed by residues 78 - 92 (chain A) in PDB entry 3BYH
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 ASN 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 5.3 6.0 - - - +
68A LYS* 2.6 36.8 - - + +
70A PRO* 3.6 4.0 + - + +
76A VAL* 3.5 10.8 - - - +
77A THR* 1.3 80.2 + - - +
79A TRP* 1.3 59.7 + - - +
80A ASP* 3.9 4.1 + - - +
81A ASP* 2.9 43.7 + - - +
82A MET* 3.1 20.1 + - - +
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Residues in contact with TRP 79 (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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76A VAL* 3.7 43.1 + - + -
77A THR 4.1 4.7 + - - -
78A ASN* 1.3 73.9 - - - +
80A ASP* 1.3 64.7 + - - +
82A MET* 3.6 4.9 + - + +
83A GLU* 3.0 29.4 + - - +
86A TRP* 4.1 20.4 - + - -
115A ASN* 4.1 35.0 - - + +
118A LYS* 3.4 48.1 - - + +
119A MET* 4.2 13.2 - - + -
122A ILE* 3.5 29.4 - - + -
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Residues in contact with ASP 80 (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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78A ASN* 3.6 5.1 + - - +
79A TRP* 1.3 79.4 - - - +
81A ASP* 1.3 62.5 + - - +
83A GLU* 3.1 16.6 + - + +
84A LYS* 2.9 38.8 + - - +
118A LYS* 5.7 0.5 + - - -
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Residues in contact with ASP 81 (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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35A VAL* 3.8 13.5 - - + -
37A ARG* 3.5 25.3 - - - +
51A ASP* 3.0 10.7 - - - +
52A SER* 2.3 42.7 + - - -
68A LYS* 4.3 3.1 - - - +
70A PRO* 4.2 3.6 - - - -
78A ASN* 2.9 28.1 + - + +
80A ASP* 1.3 77.7 - - - +
82A MET* 1.3 64.5 + - - +
84A LYS* 3.3 12.2 + - - +
85A ILE* 3.1 23.6 + - - +
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Residues in contact with MET 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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12A ASN* 3.2 27.8 - - - +
17A CYS* 4.7 0.2 - - - -
70A PRO* 3.8 7.9 - - + +
71A ILE* 3.4 38.1 - - + -
76A VAL* 3.5 23.8 - - + -
78A ASN 3.1 20.3 + - - +
79A TRP* 3.9 7.9 - - + +
81A ASP* 1.3 75.0 - - - +
83A GLU* 1.3 62.9 + - - +
85A ILE* 2.8 43.8 + - + +
86A TRP* 3.1 48.6 + - + +
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Residues in contact with GLU 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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79A TRP 3.0 20.9 + - - +
80A ASP* 3.1 17.6 + - + +
82A MET* 1.3 75.0 - - - +
84A LYS* 1.3 64.9 + - + +
86A TRP* 3.3 10.2 + - - +
87A HIS* 3.1 23.2 + - - +
118A LYS* 4.5 6.1 + - - -
122A ILE* 3.9 37.8 - - + +
126A THR* 3.9 22.1 + - + +
127A PHE* 4.0 7.8 - - + -
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Residues in contact with LYS 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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49A GLN* 4.5 6.5 + - - -
50A LYS* 4.1 15.5 - - + +
51A ASP* 3.2 33.0 - - - +
52A SER* 2.6 38.6 - - - +
54A VAL* 5.5 0.4 - - - -
80A ASP* 2.9 32.6 + - + +
81A ASP* 3.4 8.5 - - - +
83A GLU* 1.3 79.2 - - + +
85A ILE* 1.3 61.8 + - - +
86A TRP 3.2 0.2 + - - -
87A HIS* 3.3 7.1 + - - +
88A HIS* 3.0 23.5 + - - +
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Residues in contact with ILE 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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17A CYS* 3.9 16.6 - - - -
31A PHE* 4.0 10.1 - - + -
33A SER* 4.2 12.1 - - - +
35A VAL* 2.3 40.4 - - + -
54A VAL* 2.9 33.2 - - + -
70A PRO* 3.6 4.3 - - + -
71A ILE* 5.0 0.2 - - + -
81A ASP 3.1 7.2 + - - +
82A MET* 2.8 34.7 + - + +
84A LYS* 1.3 75.2 - - - +
86A TRP* 1.3 62.0 + - + +
88A HIS* 3.2 7.7 + - - +
89A THR* 2.8 31.8 + - - +
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Residues in contact with TRP 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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10A VAL* 3.7 21.2 - - + +
12A ASN* 2.9 39.2 + - - -
76A VAL* 5.6 1.6 - - + -
79A TRP* 4.1 17.5 - + - -
82A MET* 3.1 48.0 + - + +
83A GLU* 3.8 7.4 - - - +
85A ILE* 1.3 77.4 - - + +
87A HIS* 1.3 62.6 + - - +
89A THR* 2.8 28.8 + - - -
90A PHE* 3.1 15.1 + + + -
105A LEU* 4.4 11.4 - - + -
119A MET* 4.2 28.0 - - + -
122A ILE* 4.1 20.9 - - + -
123A MET* 3.5 27.4 - - + -
127A PHE* 3.9 12.1 - + + -
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Residues in contact with HIS 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 GLU 3.1 12.5 + - - +
84A LYS* 3.4 11.7 - - - +
86A TRP* 1.3 73.3 - - - +
88A HIS* 1.3 58.1 + - - +
90A PHE* 4.5 0.2 - - - -
91A TYR* 2.9 78.1 + + + +
92A ASN* 5.4 3.8 - - - -
127A PHE* 3.7 18.9 - - + -
467B LYS* 5.1 9.0 + - + +
468B PHE 5.4 2.7 + - - -
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Residues in contact with HIS 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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31A PHE* 4.2 22.0 - + - -
54A VAL* 4.9 7.4 - - + +
84A LYS 3.0 12.7 + - - +
85A ILE* 3.3 9.2 - - - +
87A HIS* 1.3 73.0 - - - +
89A THR* 1.3 58.3 + - - +
92A ASN* 3.0 10.7 + - + -
93A GLU* 2.7 53.4 + - - +
469B SER* 2.5 44.2 + - - -
471B VAL* 2.6 58.9 - - + +
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Residues in contact with THR 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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10A VAL* 3.9 22.5 - - + +
17A CYS* 5.7 0.3 - - - -
19A ALA* 3.7 29.8 - - + -
31A PHE* 3.5 18.5 - - + -
85A ILE* 2.8 18.5 + - - +
86A TRP* 2.8 27.0 + - - -
88A HIS* 1.3 73.0 - - - +
90A PHE* 1.3 58.9 + - + +
93A GLU* 3.3 8.1 + - - +
94A LEU* 2.7 41.6 + - + +
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Residues in contact with PHE 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 LEU* 3.3 35.4 - - + -
10A VAL* 4.5 17.9 - - + -
86A TRP* 3.1 31.1 + + + -
87A HIS* 4.1 1.8 - - - +
89A THR* 1.3 78.1 - - + +
91A TYR* 1.3 61.7 + + + +
94A LEU* 4.8 1.1 - - + -
95A ARG 2.8 29.8 + - - -
96A VAL* 2.8 24.1 + - + +
98A PRO* 3.6 33.4 - - + -
103A VAL* 4.0 17.3 - - + -
105A LEU* 5.6 0.4 - - + -
123A MET* 4.0 30.1 - - + -
127A PHE* 4.2 18.2 - + - -
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Residues in contact with TYR 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 HIS* 2.9 68.3 + + + +
90A PHE* 1.3 72.8 - - + +
92A ASN* 1.3 49.6 - - - +
95A ARG* 4.6 1.8 - - - +
96A VAL 4.0 9.6 - - - -
97A ALA* 5.2 1.3 - - - -
98A PRO* 3.7 32.8 - - + +
99A GLU* 4.8 3.9 + - - -
127A PHE* 4.1 20.7 + + - -
467B LYS* 2.7 40.8 - - + +
468B PHE* 2.4 9.2 - - - -
469B SER* 2.1 25.2 + - - -
492B GLN* 2.5 11.1 + - - -
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Residues in contact with ASN 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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87A HIS* 5.4 3.2 - - - -
88A HIS* 3.0 18.0 + - + +
91A TYR* 1.3 73.2 + - - +
93A GLU* 1.3 68.0 + - - +
94A LEU 3.9 0.2 - - - -
95A ARG* 3.5 1.1 - - - +
468B PHE 1.7 24.7 + - - +
469B SER* 0.8 347.7 + - - +
470B LEU* 2.2 14.6 + - - +
471B VAL* 3.9 4.2 - - - +
488B GLY* 5.0 2.8 - - - +
492B GLN* 2.9 23.3 - - - +
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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