Contacts of the strand formed by residues 100 - 108 (chain r) in PDB entry 5GJQ
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 100 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46r CYS* 3.7 17.0 - - - -
47r VAL 3.5 2.0 - - - -
52r ASP* 3.7 13.5 - - + +
53r THR* 3.6 33.0 - - + -
56r PHE* 3.8 18.6 - - + -
88r LEU* 3.6 31.6 - - + +
98r TYR* 3.0 6.5 + - + +
99r HIS* 1.3 83.0 - - - +
101r ASN* 1.3 64.0 + - - +
102r LEU* 3.7 9.7 - - + +
119r ASP 3.8 0.3 - - - +
120r TYR* 3.1 22.2 + - - +
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Residues in contact with ASN 101 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4r LEU* 4.6 0.2 - - - +
45r LEU 4.0 0.2 - - - +
46r CYS* 4.2 0.5 - - - -
47r VAL* 2.8 45.9 + - + +
48r GLY* 4.7 3.6 - - - -
99r HIS 4.2 0.2 - - - -
100r VAL* 1.3 72.7 - - - +
102r LEU* 1.3 64.2 + - - +
118r MET 3.7 2.7 - - - -
119r ASP* 3.5 10.5 - - - +
120r TYR* 2.9 41.2 + - - +
132r HIS* 3.5 34.2 + - + +
133r GLY 5.9 1.4 - - - +
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Residues in contact with LEU 102 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4r LEU* 4.9 0.7 - - - -
44r LEU* 3.7 27.1 - - + -
45r LEU 3.2 12.6 - - - +
46r CYS* 4.2 9.2 - - - -
56r PHE* 3.9 23.6 - - + -
84r THR* 4.1 14.4 - - - +
88r LEU* 4.1 9.6 - - + -
100r VAL* 3.7 25.8 - - + +
101r ASN* 1.3 79.8 - - - +
103r LEU* 1.3 60.7 + - - +
104r LEU* 5.5 2.7 - - + -
116r TYR 3.9 0.2 - - - +
118r MET* 3.0 55.3 + - + +
132r HIS* 3.3 12.0 - - - -
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Residues in contact with LEU 103 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4r LEU* 4.1 11.2 - - + +
5r ILE 4.0 24.7 - - - +
6r GLY* 4.1 15.9 - - - +
15r VAL* 5.8 3.1 - - + -
43r LEU 3.9 0.5 - - - +
44r LEU* 3.6 5.5 - - - +
45r LEU* 2.9 46.4 + - + +
102r LEU* 1.3 79.3 - - - +
104r LEU* 1.3 63.5 + - - +
105r ALA* 4.1 0.9 - - + -
115r LEU* 4.5 12.8 - - + -
116r TYR 3.3 13.5 - - - +
117r TYR* 4.0 17.5 - - + -
130r ALA* 4.2 11.2 - - + +
131r ALA* 4.1 15.5 - - - +
132r HIS* 3.8 15.9 - - - +
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Residues in contact with LEU 104 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38r MET* 4.7 3.8 - - + -
42r ILE* 3.8 23.6 - - + -
43r LEU 3.6 6.3 - - - +
44r LEU* 4.1 14.4 - - + -
77r PRO* 3.6 24.5 - - + +
80r ALA* 4.2 2.0 - - + -
81r ALA* 3.5 30.1 - - + +
84r THR* 3.9 20.4 - - + +
102r LEU* 5.5 3.1 - - + -
103r LEU* 1.3 76.8 - - - +
105r ALA* 1.3 64.8 + - - +
114r ALA 3.8 0.7 - - - +
115r LEU* 3.5 3.6 - - - -
116r TYR* 2.9 51.5 + - + +
118r MET* 5.7 4.9 - - + -
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Residues in contact with ALA 105 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13r VAL* 3.7 24.7 - - + -
15r VAL* 3.9 18.4 - - + -
42r ILE* 3.5 6.4 - - - +
43r LEU* 2.9 35.7 + - + +
45r LEU* 5.8 0.7 - - + -
103r LEU 4.1 0.8 - - - -
104r LEU* 1.3 79.2 - - - +
106r GLY* 1.3 60.3 + - - +
114r ALA 3.4 5.4 - - - -
115r LEU* 4.1 4.3 - - + -
183r ILE* 3.8 16.1 - - + +
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Residues in contact with GLY 106 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13r VAL* 3.1 14.3 - - - +
41r LYS 3.1 12.8 - - - -
77r PRO* 3.7 19.0 - - - +
105r ALA* 1.3 77.8 - - - +
107r TYR* 1.3 60.8 + - - -
113r PRO* 3.4 0.2 - - - +
114r ALA 2.9 31.1 + - - -
183r ILE* 4.1 7.2 - - - -
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Residues in contact with TYR 107 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11r ASP* 3.8 29.6 - - + +
12r TYR* 4.8 0.4 - - - -
13r VAL* 5.2 0.2 - - + -
41r LYS* 3.2 28.7 + - + +
77r PRO* 3.8 5.8 - - - +
106r GLY* 1.3 75.6 - - - +
108r ASP* 1.3 76.8 + - - +
109r GLU* 4.2 9.0 + - - -
112r GLY* 3.5 6.0 - - - -
113r PRO* 3.7 32.1 - - + -
183r ILE* 4.4 8.0 - - + +
184r ASP* 3.3 30.7 - - - +
185r LYS* 3.5 28.8 - - + +
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Residues in contact with ASP 108 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141j LYS* 4.5 6.6 + - - -
74r GLU 5.7 1.0 - - - +
75r LEU 5.2 1.9 - - - +
76r SER* 4.1 21.4 - - - -
77r PRO* 3.9 16.9 - - + +
107r TYR* 1.3 91.8 - - - +
109r GLU* 1.3 74.8 + - - +
110r HIS* 3.1 16.3 + - - +
111r GLU* 3.6 32.9 + - + +
112r GLY* 2.9 25.6 + - - +
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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