Contacts of the strand formed by residues 101 - 110 (chain X) in PDB entry 3BIB
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 VAL 101 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20X TYR* 4.1 25.1 - - + +
90X CYS 3.7 1.7 - - - +
91X ARG* 3.6 2.4 - - - -
92X ILE* 2.9 49.1 + - + +
94X VAL* 4.3 6.7 - - + +
99X ASN 4.3 7.2 - - - +
100X ASP* 1.3 69.0 - - - +
102X LYS* 1.3 66.1 + - - +
103X LYS* 5.4 4.2 - - + +
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Residues in contact with LYS 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X CYS* 3.9 23.8 + - + -
38X PRO 3.8 15.6 + - - +
39X ASN* 4.1 20.6 + - - +
90X CYS 3.8 3.8 - - - -
91X ARG* 3.6 38.4 - - + +
100X ASP* 3.3 17.1 + - + +
101X VAL* 1.3 78.2 - - - +
103X LYS* 1.3 61.9 + - - +
118X PSF 5.3 2.9 + - - +
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Residues in contact with LYS 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP* 5.4 8.4 + - + -
17X PRO* 2.7 36.7 + - - +
18X CYS* 3.8 19.8 - - - +
19X HIS* 4.9 3.2 + - - +
37X CYS* 3.8 1.2 - - - -
88X TYR 3.7 0.2 - - - +
89X CYS* 3.6 2.8 - - - -
90X CYS* 2.9 40.7 + - + +
101X VAL* 5.4 5.4 - - + +
102X LYS* 1.3 76.4 - - - +
104X ASN* 1.3 73.8 + - - +
105X VAL* 3.8 17.8 + - + +
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Residues in contact with ASN 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP* 4.6 11.3 + - - +
36X SER* 3.1 24.4 - - - +
37X CYS* 2.8 41.7 + - - +
87X VAL* 3.7 11.9 - - + -
88X TYR 3.3 6.7 + - - -
103X LYS* 1.3 79.1 - - - +
105X VAL* 1.3 64.3 + - - +
106X ARG 4.3 0.4 + - - -
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Residues in contact with VAL 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP* 3.9 16.6 - - + +
6X ILE* 4.0 21.8 - - + -
16X LEU* 4.3 18.6 - - + -
17X PRO* 4.3 11.7 - - + +
32X TRP* 4.4 16.2 - - + -
86X GLY 3.6 0.9 - - - +
87X VAL* 3.4 3.6 - - - -
88X TYR* 2.7 41.6 + - + +
103X LYS* 3.8 28.7 - - + +
104X ASN* 1.3 79.4 - - - +
106X ARG* 1.3 72.0 + - - +
107X LEU 3.8 0.2 + - - -
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Residues in contact with ARG 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP 3.0 14.1 + - - +
5X THR* 3.4 22.6 - - + +
6X ILE* 2.9 26.3 + - - -
86X GLY* 3.5 18.3 - - - +
87X VAL* 3.3 32.8 - - + +
104X ASN 4.3 0.2 - - - -
105X VAL* 1.3 77.8 - - - +
107X LEU* 1.3 68.4 + - - +
108X GLU* 4.8 2.0 - - + +
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Residues in contact with LEU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ILE* 3.5 19.5 - - + +
8X GLY 4.4 0.4 - - - +
14X VAL* 3.8 36.1 - - + -
16X LEU* 4.1 17.3 - - + -
77X ILE* 4.2 4.7 - - + -
80X THR* 4.8 0.4 - - + -
84X ASP* 3.6 25.1 - - + +
85X SER* 3.4 7.1 + - - -
86X GLY* 2.8 39.0 + - - +
88X TYR* 4.0 18.8 - - + +
106X ARG* 1.3 77.8 + - - +
108X GLU* 1.3 67.3 + - - +
109X LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X THR* 4.3 13.9 - - + +
6X ILE 2.9 13.1 + - - +
7X ILE* 3.4 16.5 - - + +
8X GLY 3.0 23.6 + - - -
85X SER* 4.2 2.0 - - - -
106X ARG* 4.1 3.3 - - + -
107X LEU* 1.3 77.6 - - - +
109X LEU* 1.3 69.3 + - - +
110X ARG* 3.0 38.3 + - - +
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Residues in contact with LEU 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X GLY* 3.4 20.6 - - - +
9X PHE 4.3 0.7 - - - +
10X LEU* 4.2 15.3 - - + -
14X VAL* 4.1 3.6 - - + -
80X THR* 3.7 32.8 - - + +
81X ASN 3.2 30.7 - - - +
82X ARG* 4.6 13.5 + - + +
84X ASP* 4.1 4.9 - - + -
85X SER* 3.7 29.5 + - - +
107X LEU* 4.0 18.6 - - + -
108X GLU* 1.3 86.0 - - - +
110X ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ILE* 3.6 31.9 - - + +
8X GLY 2.9 10.8 + - - +
9X PHE* 3.6 14.8 - - + -
10X LEU* 3.0 29.7 + - - +
82X ARG* 5.9 0.2 - - - +
108X GLU* 3.0 29.7 + - - +
109X LEU* 1.3 78.7 - - - +
111X ARG* 1.3 67.7 + - - +
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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