Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 3CB4
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 PHE 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PRO* 4.2 27.1 - - + -
81A HIS* 3.2 20.1 + - + +
83A ASP* 1.3 77.4 - - + +
85A SER* 1.3 63.6 + - - +
86A TYR 3.0 3.6 + - - -
87A GLU* 3.2 30.1 + - + -
88A VAL* 2.8 22.3 + - - +
343A LEU* 3.7 21.1 - - + -
346A LEU* 4.4 16.2 - - + -
347A HIS* 4.0 32.8 - + + -
350A ILE* 4.2 22.4 - - + -
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Residues in contact with SER 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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81A HIS 3.8 0.6 + - - -
82A VAL* 3.3 32.8 + - - +
83A ASP 3.2 3.1 + - - -
84A PHE* 1.3 76.8 - - - +
86A TYR* 1.3 60.4 + - - +
88A VAL* 3.4 9.2 - - - +
89A SER* 3.2 21.7 + - - -
115A ASN* 6.0 0.2 - - - -
118A THR* 6.1 1.0 - - - +
471A ASN* 5.4 8.7 - - - +
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Residues in contact with TYR 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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83A ASP 5.3 0.2 + - - -
84A PHE 3.2 0.8 - - - -
85A SER* 1.3 75.3 - - - +
87A GLU* 1.3 74.2 + - + +
88A VAL 3.0 1.1 - - - -
89A SER* 2.8 30.5 + - - -
90A ARG* 3.0 24.2 + - + +
270A VAL* 2.9 36.1 + - + -
271A GLY* 3.5 5.0 - - - -
287A GLY 3.5 19.5 - - - -
288A PHE* 3.3 9.4 - - - -
289A LYS* 2.9 59.4 + - + -
291A VAL* 3.5 26.0 - - + -
343A LEU* 6.4 0.7 - - + -
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Residues in contact with GLU 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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79A PRO* 5.2 9.0 - - + +
84A PHE* 3.2 37.9 + - + +
86A TYR* 1.3 81.3 - - + +
88A VAL* 1.3 62.7 + - - +
90A ARG* 3.4 2.3 + - - +
91A SER* 3.2 25.5 + - - -
196A ILE 4.9 2.0 - - - +
197A ASP* 5.1 7.4 - - - +
270A VAL* 4.3 33.8 - - + +
322A ALA* 5.8 2.6 - - - +
323A SER* 3.8 18.0 + - - -
343A LEU* 4.4 2.8 - - + +
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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
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78A THR* 3.9 7.1 - - + +
79A PRO* 3.4 40.2 - - + +
81A HIS 4.3 6.5 - - - +
84A PHE 2.8 21.2 + - - +
85A SER* 3.4 11.4 - - - +
87A GLU* 1.3 76.1 - - - +
89A SER* 1.3 59.0 + - - +
91A SER* 3.3 8.2 + - - -
92A LEU* 3.0 42.2 + - + +
115A ASN* 3.4 32.5 - - - +
118A THR* 5.2 2.7 - - - +
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Residues in contact with SER 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 SER 3.2 8.9 + - - -
86A TYR* 2.8 30.1 + - - -
88A VAL* 1.3 75.9 - - - +
90A ARG* 1.3 86.0 + - - +
92A LEU* 3.5 11.9 + - - +
93A ALA* 3.0 21.1 + - - +
118A THR* 5.9 7.9 - - - -
122A MET* 3.8 11.2 - - - +
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Residues in contact with ARG 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 TYR* 3.0 46.8 + - + +
87A GLU 3.9 6.1 - - - +
89A SER* 1.3 108.6 + - - +
91A SER* 1.3 63.5 + - - +
93A ALA* 3.3 21.0 + - - +
94A ALA* 3.4 8.8 + - - +
122A MET* 3.8 17.6 - - - +
194A LEU* 3.5 23.6 - - + +
195A ILE 4.7 3.8 - - - +
196A ILE* 4.8 5.1 - - - +
270A VAL* 3.9 13.7 - - + -
271A GLY* 3.6 26.4 + - - +
286A PRO 3.3 24.9 + - - -
287A GLY* 3.5 20.5 + - - -
288A PHE 4.5 0.2 - - - +
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Residues in contact with SER 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 SER* 5.6 0.7 - - - -
76A ILE* 3.6 20.0 - - - +
77A ASP 4.0 10.6 + - - -
78A THR* 5.2 6.5 - - - -
79A PRO* 5.5 2.2 - - - +
87A GLU 3.2 14.4 + - - -
88A VAL* 3.5 10.1 - - - -
90A ARG* 1.3 76.9 - - - +
92A LEU* 1.3 60.6 + - - +
94A ALA* 3.2 13.7 + - - +
95A CYS* 3.3 17.5 - - - -
196A ILE* 3.2 28.3 + - - +
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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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8A SER* 3.4 23.8 - - - +
10A ILE* 5.0 5.8 - - + -
78A THR* 5.0 7.2 - - + +
88A VAL* 3.0 41.3 + - + +
89A SER* 3.8 9.0 - - - +
90A ARG 3.3 0.2 - - - -
91A SER* 1.3 72.9 - - - +
93A ALA* 1.3 61.6 + - - +
94A ALA 3.0 5.6 - - - -
95A CYS* 3.1 16.2 + - - +
98A ALA* 4.8 3.4 - - + -
115A ASN* 4.3 8.3 - - + +
118A THR* 4.4 8.5 - - - +
119A ALA* 4.1 30.5 - - + +
122A MET* 4.0 12.9 - - - +
124A LEU* 3.4 34.4 - - + +
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Residues in contact with ALA 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 SER 3.0 16.6 + - - +
90A ARG* 3.6 24.0 - - - +
91A SER 3.3 0.4 - - - -
92A LEU* 1.3 76.3 - - - +
94A ALA* 1.3 54.7 + - - +
95A CYS 3.2 4.5 + - - +
122A MET* 3.7 19.2 - - + +
124A LEU* 5.8 0.7 - - - -
194A LEU* 3.8 12.8 - - + -
213A LYS* 2.7 34.1 + - - +
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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
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6A ASN* 3.6 10.7 - - - +
76A ILE* 4.7 5.1 - - + +
90A ARG 3.4 2.1 + - - +
91A SER 3.2 13.2 + - - +
92A LEU 3.0 1.0 - - - -
93A ALA* 1.3 79.0 - - - +
95A CYS* 1.3 58.8 + - - +
96A GLU* 4.8 0.9 - - - -
194A LEU* 3.9 7.6 - - + -
196A ILE* 3.8 27.8 - - + -
211A ARG* 3.3 46.8 + - + +
213A LYS* 4.6 0.4 - - - +
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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