Contacts of the strand formed by residues 70 - 76 (chain m) 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 70 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65m HIS* 3.8 1.4 - - - -
66m VAL* 3.0 25.8 + - + -
67m ASP 2.8 32.5 + - - +
68m ASN 3.6 0.2 - - - -
69m HIS* 1.3 113.4 - - + +
71m GLY* 1.3 68.2 - - - +
88m MET* 4.7 0.9 - - + -
92m CYS* 4.7 2.7 - - - -
103m LEU 3.9 6.7 - - - +
105m VAL* 3.9 28.7 - - + -
108m LEU* 3.6 31.2 - - + -
134m ILE* 4.2 13.0 - - + -
135m ALA 3.6 3.1 - - - +
136m GLY* 4.5 1.1 - - - -
221m PHE* 4.2 4.8 - - - +
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Residues in contact with GLY 71 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46m LEU* 3.9 6.9 - - - +
64m LEU 3.4 7.4 - - - -
66m VAL 4.4 0.9 - - - -
70m ILE* 1.3 74.3 - - - +
72m ILE* 1.3 67.5 + - - +
134m ILE* 3.7 1.6 - - - +
135m ALA 2.9 33.8 + - - -
221m PHE* 3.3 27.0 - - - -
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Residues in contact with ILE 72 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46m LEU* 3.6 4.6 - - - +
63m ILE* 3.3 7.4 - - - +
64m LEU* 2.8 68.3 + - + +
66m VAL* 4.1 7.0 - - + -
70m ILE* 4.8 0.2 - - + -
71m GLY* 1.3 79.1 - - - +
73m SER* 1.3 60.8 - - - +
74m ILE* 4.2 2.0 - - + -
81m ALA 5.0 1.6 - - - +
85m CYS* 4.1 12.6 - - + -
88m MET* 3.4 44.4 - - + -
132m LEU* 4.2 21.5 - - + -
133m LEU 3.2 7.0 - - - +
134m ILE* 4.1 16.2 - - + -
221m PHE* 4.4 0.2 - - - -
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Residues in contact with SER 73 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35m THR* 2.6 35.4 + - - -
46m LEU* 3.9 18.2 - - - -
48m ALA* 3.9 8.0 - - - +
62m LYS 3.2 12.9 + - - -
63m ILE* 4.3 1.7 - - - +
72m ILE* 1.3 75.9 - - - +
74m ILE* 1.3 64.0 + - - +
131m GLY 3.8 0.2 - - - +
132m LEU* 3.5 6.1 - - - -
133m LEU* 2.8 37.7 + - - +
161m ILE* 4.6 1.4 - - - +
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Residues in contact with ILE 74 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439M ALA* 5.3 3.8 - - + -
35m THR* 4.3 5.6 - - - +
61m LYS 4.2 15.0 - - - +
62m LYS* 3.1 41.4 + - + +
64m LEU* 3.7 26.9 - - + -
72m ILE* 4.2 4.3 - - + -
73m SER* 1.3 79.3 - - - +
75m ALA* 1.3 64.8 + - - +
76m GLY 5.3 1.3 - - - +
78m THR* 4.3 23.1 - - + -
81m ALA* 3.7 31.4 - - + -
130m VAL* 4.5 0.9 - - + -
131m GLY 3.7 3.1 - - - -
132m LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 75 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439M ALA* 4.3 5.8 - - - -
29m VAL* 3.6 29.3 - - + +
32m GLY* 4.7 1.1 - - - -
33m SER 4.6 11.0 - - - +
35m THR* 4.7 0.7 - - + -
74m ILE* 1.3 77.7 - - - +
76m GLY* 1.3 58.6 + - - +
130m VAL* 3.6 2.4 - - - +
131m GLY 2.9 31.6 + - - -
161m ILE* 3.7 30.1 - - + -
162m GLY 4.7 1.6 - - - +
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Residues in contact with GLY 76 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438M TYR* 3.8 7.8 - - - -
439M ALA* 2.9 35.5 + - - +
28m ALA 3.6 19.3 - - - -
32m GLY* 4.3 1.6 - - - -
74m ILE* 5.3 1.9 - - - +
75m ALA* 1.3 74.7 - - - +
77m LEU* 1.3 67.1 + - - -
78m THR* 3.2 2.1 + - - +
129m GLY 3.6 7.6 - - - -
130m VAL* 4.3 2.2 - - - +
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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