Contacts of the strand formed by residues 71 - 77 (chain i) 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 ILE 71 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66i PRO* 3.9 2.8 - - - +
67i ILE* 3.0 31.7 + - + -
68i THR* 3.6 15.0 + - - +
69i LYS 3.8 0.6 - - - -
70i HIS* 1.3 109.8 - - + +
72i GLY* 1.3 62.8 + - - +
104i ILE* 3.6 16.2 - - + +
106i THR* 3.7 27.8 - - + +
109i LEU* 3.6 31.9 - - + -
135i ILE* 3.7 13.7 - - + -
136i CYS 3.3 11.0 - - - +
217i PHE* 3.9 7.3 - - - +
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Residues in contact with GLY 72 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45i LEU* 4.0 7.4 - - - -
65i GLU 3.5 6.7 - - - -
67i ILE* 4.6 0.4 - - - -
71i ILE* 1.3 76.3 - - - +
73i LEU* 1.3 63.2 - - - -
134i LEU 3.7 0.2 - - - +
135i ILE* 3.2 8.5 - - - +
136i CYS* 3.0 34.2 + - - -
217i PHE* 3.4 24.2 - - - -
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Residues in contact with LEU 73 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45i LEU* 4.1 3.6 - - - +
64i VAL* 3.3 2.3 - - - +
65i GLU 2.9 32.8 + - - +
67i ILE* 3.6 30.3 - - + -
72i GLY* 1.3 75.8 - - - +
74i VAL* 1.3 69.3 + - - +
82i TYR* 3.2 12.9 + - + +
85i LEU 5.1 1.1 - - - +
86i VAL* 3.7 27.4 - - + +
89i ALA* 4.9 4.7 - - + -
133i LEU* 3.9 25.1 - - + -
134i LEU 3.3 16.2 - - - +
135i ILE* 3.4 27.4 - - + -
217i PHE* 4.4 1.4 - - - -
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Residues in contact with VAL 74 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34i SER* 4.9 4.3 - - - +
45i LEU* 3.8 25.6 - - + -
46i ALA 4.7 5.8 - - - +
47i THR* 4.3 16.8 - - + -
63i LYS 3.6 12.3 - - - +
64i VAL* 3.5 32.5 - - + -
73i LEU* 1.3 83.3 - - - +
75i TYR* 1.3 64.4 + - - +
82i TYR* 3.9 3.1 - - - -
133i LEU* 3.6 3.5 - - - -
134i LEU* 2.9 53.5 + - + +
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Residues in contact with TYR 75 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LYS 3.6 15.3 + - - -
32i ALA 4.3 1.4 - - - +
34i SER* 3.0 19.4 + - - -
47i THR* 4.2 4.5 + - - -
62i HIS 5.7 0.2 - - - -
63i LYS* 3.5 45.3 + - + +
74i VAL* 1.3 80.4 - - - +
76i SER* 1.3 65.2 + - - +
77i GLY 3.6 28.9 - - - -
78i MET 3.7 19.1 - - - -
79i GLY* 3.8 14.5 - - - -
82i TYR* 3.3 49.4 - + + -
131i VAL* 4.1 6.3 - - + -
132i SER 3.3 10.8 - - - +
133i LEU* 4.2 0.4 - - + -
162i MET* 4.1 2.9 - - - -
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Residues in contact with SER 76 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28i VAL* 3.4 14.7 - - - +
32i ALA 3.0 25.2 + - - +
34i SER* 3.3 4.7 + - - -
75i TYR* 1.3 79.7 + - - +
77i GLY* 1.3 58.7 + - - +
131i VAL* 3.5 0.9 - - - -
132i SER 2.9 32.9 + - - -
162i MET* 3.2 35.9 + - - +
163i GLY* 3.9 12.6 - - - -
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Residues in contact with GLY 77 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K TYR 4.6 4.0 - - - -
418K LYS* 3.5 27.4 - - - +
27i ALA 3.9 19.5 - - - -
28i VAL* 4.0 2.0 - - - -
31i GLY* 4.3 9.2 - - - -
32i ALA 5.2 0.4 - - - +
75i TYR* 3.6 5.1 - - - -
76i SER* 1.3 76.4 - - - +
78i MET* 1.3 64.5 + - - -
79i GLY 3.7 0.2 + - - -
130i GLY 3.1 10.5 - - - -
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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