Contacts of the helix formed by residues 84 - 95 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D PRO* 4.5 24.0 - - + -
81D HIS* 3.0 28.9 + - + +
83D ASP* 1.3 80.9 - - + +
85D SER* 1.3 62.9 + - - +
86D TYR* 3.1 3.8 + - - -
87D GLU* 3.2 33.5 + - + +
88D VAL* 2.9 28.1 + - + +
343D LEU* 3.6 28.3 - - + -
346D LEU* 4.9 7.9 - - + -
347D HIS* 4.2 16.8 - + + -
350D ILE* 4.7 19.5 - - + -
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS 3.7 0.9 + - - -
82D VAL* 3.3 37.0 + - - +
83D ASP 3.3 4.0 + - - -
84D PHE* 1.3 75.4 - - - +
86D TYR* 1.3 61.7 + - - +
88D VAL* 3.7 5.9 + - - +
89D SER* 3.2 22.3 + - - -
118D THR* 6.0 1.6 - - - +
471D ASN* 5.6 5.2 - - - +
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Residues in contact with TYR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ASP 5.4 0.2 + - - -
84D PHE 3.2 0.6 - - - -
85D SER* 1.3 76.4 - - - +
87D GLU* 1.3 73.8 + - + +
89D SER* 2.7 26.6 + - - -
90D ARG* 2.9 31.0 + - + +
270D VAL* 2.9 37.7 + - + -
271D GLY* 3.2 12.6 - - - -
287D GLY 3.1 22.0 - - - -
288D PHE* 3.5 4.9 - - - -
289D LYS* 3.2 50.9 + - + -
291D VAL* 3.7 28.0 - - + -
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PRO* 5.4 6.9 - - + +
84D PHE* 3.2 34.9 + - + +
86D TYR* 1.3 83.5 - - + +
88D VAL* 1.3 61.2 + - + +
90D ARG* 3.3 8.4 + - - +
91D SER* 3.0 25.0 + - - -
196D ILE 5.0 3.1 - - - +
197D ASP* 5.4 8.6 - - - +
270D VAL* 4.5 25.0 - - + +
322D ALA* 5.5 6.8 + - - +
323D SER* 5.3 4.9 + - - -
343D LEU* 5.4 2.9 - - + +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D THR* 3.8 22.9 - - + -
79D PRO* 3.3 31.9 - - + +
81D HIS 4.3 7.0 - - - +
84D PHE* 2.9 28.7 + - + +
85D SER* 3.7 5.8 - - - +
87D GLU* 1.3 75.5 - - - +
89D SER* 1.3 57.9 + - - +
91D SER* 3.1 9.0 + - - -
92D LEU* 2.9 44.3 + - + +
115D ASN* 3.9 20.0 - - - +
118D THR* 5.3 1.6 - - - +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D SER 3.2 9.8 + - - -
86D TYR* 2.7 29.1 + - - -
88D VAL* 1.3 78.3 - - - +
90D ARG* 1.3 86.4 + - - +
92D LEU* 3.6 13.5 + - - +
93D ALA* 3.1 19.6 + - - +
118D THR* 5.9 7.2 - - - -
122D MET* 4.1 9.6 - - - +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TYR* 2.9 42.1 + - + +
87D GLU 3.6 7.6 - - - +
89D SER* 1.3 112.9 + - - +
91D SER* 1.3 63.9 + - - +
92D LEU 3.2 0.2 - - - -
93D ALA* 3.2 31.4 + - - +
94D ALA* 3.4 9.7 + - - +
122D MET* 4.4 8.9 - - - +
194D LEU* 3.7 18.4 - - + +
195D ILE 4.7 3.8 - - - +
196D ILE* 4.6 8.3 - - - +
270D VAL* 3.9 17.3 - - + -
271D GLY* 3.6 27.7 + - - +
286D PRO 3.6 22.6 + - - -
287D GLY* 3.8 15.7 + - - -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 5.1 1.6 - - - -
76D ILE* 3.5 22.4 - - - +
77D ASP 4.2 6.9 + - - -
78D THR* 5.0 7.9 - - - -
79D PRO* 5.9 1.5 - - - +
87D GLU 3.0 13.8 + - - -
88D VAL* 3.1 11.2 + - - -
90D ARG* 1.3 75.0 - - - +
92D LEU* 1.3 60.5 + - - +
94D ALA* 3.4 9.9 - - - +
95D CYS* 3.4 20.1 - - - -
196D ILE* 3.4 26.6 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 3.4 21.5 - - - +
10D ILE* 5.1 5.6 - - + -
78D THR* 5.1 5.2 - - + +
88D VAL* 2.9 37.5 + - + +
89D SER* 3.8 10.3 - - - +
90D ARG 3.2 0.2 - - - -
91D SER* 1.3 74.0 - - - +
93D ALA* 1.3 61.2 + - - +
94D ALA 3.1 2.2 - - - -
95D CYS* 3.0 26.2 + - - +
98D ALA* 4.8 4.9 - - + -
115D ASN* 4.1 16.6 - - + +
118D THR* 4.2 12.8 - - - +
119D ALA* 4.2 20.4 - - + +
122D MET* 4.2 11.2 - - - -
124D LEU* 3.5 28.7 - - + +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER 3.1 18.6 + - - +
90D ARG* 3.2 28.0 + - - +
92D LEU* 1.3 76.2 - - - +
94D ALA* 1.3 55.9 + - - +
95D CYS 3.3 3.9 + - - +
122D MET* 3.7 18.1 - - + +
124D LEU* 5.7 0.2 - - - -
194D LEU* 3.8 10.8 - - + -
213D LYS* 2.8 33.5 + - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN* 3.8 6.6 - - - +
76D ILE* 4.1 10.5 - - + -
90D ARG 3.4 4.1 + - - +
91D SER* 3.4 12.8 - - - +
92D LEU 3.1 0.2 - - - -
93D ALA* 1.3 79.7 - - - +
95D CYS* 1.3 58.8 + - - +
96D GLU* 4.9 0.2 - - - -
194D LEU* 3.9 4.0 - - + +
196D ILE* 3.9 26.7 - - + -
211D ARG* 3.0 52.3 + - + +
213D LYS* 4.7 0.2 - - - +
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Residues in contact with CYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN 3.4 8.3 - - - +
7D PHE* 3.4 26.5 - - - -
8D SER* 3.5 13.5 - - - +
76D ILE* 3.5 19.1 - - - -
91D SER 3.4 18.6 - - - -
92D LEU 3.0 18.2 + - - +
93D ALA 4.1 3.5 - - - +
94D ALA* 1.3 80.3 - - - +
96D GLU* 1.3 65.8 + - - +
97D GLY 3.3 18.4 - - - +
124D LEU* 3.3 13.3 - - + +
213D LYS* 5.4 0.5 + - - -
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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