Contacts of the strand formed by residues 94 - 102 (chain D) in PDB entry 3CHB
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 ARG 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLN* 5.5 0.8 + - - -
18D HIS* 5.1 7.2 - - + -
47D THR 4.0 4.9 + - - +
48D PHE* 3.3 28.5 - - + +
49D GLN 2.9 23.7 + - - -
87D VAL* 3.9 14.4 - - + -
88D TRP 3.4 16.2 - - - -
89D ASN* 3.6 35.7 + - - +
91D LYS 2.9 30.3 + - - -
92D THR* 3.2 20.0 + - - +
93D PRO* 1.3 71.5 - - - +
95D ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 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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49D GLN* 3.6 7.6 - - + -
51D GLU* 3.5 39.7 - - + +
87D VAL* 3.1 5.6 - - - -
88D TRP* 2.9 42.8 + - + -
91D LYS* 3.9 15.9 - - + +
93D PRO 3.3 0.8 + - - -
94D ARG* 1.3 72.7 - - - +
96D ILE* 1.3 64.6 + - - +
97D ALA 3.5 0.3 + - - -
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Residues in contact with ILE 96 (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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40D ILE* 4.0 12.1 - - + -
48D PHE* 3.8 29.2 - - + -
49D GLN 2.9 23.8 + - - +
50D VAL* 4.7 6.2 - - + -
51D GLU 5.8 0.5 + - - -
68D MET* 4.1 23.1 - - + -
72D LEU* 3.8 28.0 - - + -
85D LEU* 4.2 17.7 - - + -
86D CYS 3.7 4.0 - - - +
87D VAL* 4.4 2.9 - - + -
88D TRP* 3.6 4.8 - - - -
95D ALA* 1.3 73.0 - - - +
97D ALA* 1.3 59.3 + - - +
98D ALA 3.7 22.4 - - - +
31E LEU* 3.4 23.0 - - - +
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Residues in contact with ALA 97 (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 LEU* 5.7 0.7 - - + -
12D TYR* 6.1 0.9 - - + -
15D THR* 5.5 0.7 - - + -
68D MET* 4.5 0.2 - - - -
86D CYS* 2.8 33.4 + - - +
87D VAL* 4.7 0.7 - - - +
88D TRP* 3.4 37.7 - - + -
95D ALA 3.5 1.2 + - - -
96D ILE* 1.3 75.4 - - - +
98D ALA* 1.3 59.3 + - + +
30E SER* 3.5 1.0 + - - -
31E LEU* 2.9 31.2 + - - +
32E ALA* 3.6 11.1 + - + -
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Residues in contact with ALA 98 (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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5D ILE* 3.6 22.0 - - + -
8D LEU* 4.3 10.8 - - + -
68D MET* 4.0 2.7 - - - -
85D LEU* 3.5 8.0 - - - +
86D CYS* 3.0 31.4 + - + +
96D ILE* 3.7 5.2 - - - +
97D ALA* 1.3 80.0 - - - +
99D ILE* 1.3 61.3 + - - +
28E THR* 5.2 1.6 - - + -
29E GLU 3.1 14.8 - - - +
30E SER* 3.9 12.6 - - - -
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Residues in contact with ILE 99 (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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5D ILE* 3.5 4.7 - - - -
40D ILE* 5.8 0.2 - - + -
68D MET* 3.7 23.1 - - + -
71D THR* 4.3 13.9 - - + -
72D LEU* 3.6 28.0 - - + -
75D ALA* 5.4 2.0 - - + -
82D VAL* 4.0 23.1 - - + -
84D LYS 3.5 5.4 - - - +
85D LEU* 3.7 18.8 - - + -
98D ALA* 1.3 76.5 - - - +
100D SER* 1.3 72.4 + - - +
101D MET* 4.5 11.7 - - + -
27E TYR* 4.0 2.4 - - + +
28E THR* 3.2 4.2 - - - +
29E GLU* 2.9 46.2 + - + +
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Residues in contact with SER 100 (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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5D ILE* 3.6 12.3 - - - +
82D VAL* 3.7 2.3 - - - -
83D GLU* 2.7 54.4 + - - -
84D LYS* 3.0 30.5 + - - +
99D ILE* 1.3 75.0 - - - +
101D MET* 1.3 60.8 + - - +
26E SER* 5.9 1.8 - - - -
27E TYR 3.4 4.7 - - - -
28E THR* 3.4 18.4 - - - -
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Residues in contact with MET 101 (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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71D THR* 4.1 19.5 - - + -
75D ALA* 3.9 26.7 - - + -
80D ALA* 4.1 15.7 - - - -
81D LYS 3.5 15.3 - - - +
82D VAL* 4.4 5.8 - - - -
83D GLU* 4.5 0.7 - - - -
99D ILE* 4.5 11.2 - - + -
100D SER* 1.3 79.8 - - - +
102D ALA* 1.3 59.4 + - - +
26E SER* 3.2 8.5 - - - -
27E TYR* 2.8 60.3 + - + +
73E ARG* 4.8 5.2 - - + -
76E TYR* 3.4 25.5 + - + -
77E LEU* 4.3 10.1 - - + -
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Residues in contact with ALA 102 (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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21D ASN* 5.9 0.4 - - - +
81D LYS* 3.4 26.5 + - - +
83D GLU* 4.2 25.8 - - + +
101D MET* 1.3 75.4 - - - +
103D ASN* 1.3 70.4 + - - +
25E PHE* 3.8 20.4 - - + +
26E SER* 4.1 8.7 - - - -
76E TYR* 3.1 10.4 + - - -
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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