Contacts of the strand formed by residues 66 - 70 (chain n) 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 LEU 66 (chain n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47n PHE* 4.0 14.6 - - + +
49n VAL* 3.7 14.6 - - + -
64n LYS* 3.3 15.1 - - + +
65n ARG* 1.3 89.3 - - - +
67n PHE* 1.3 67.5 + - - +
68n ASN* 5.7 0.9 + - - -
75n MET 3.2 2.9 - - - +
76n ALA* 3.5 26.0 - - + -
212n GLU* 3.7 36.5 + - + +
213n LEU 3.8 14.8 - - - +
214n SER* 3.2 30.3 - - - +
224n HIS* 5.2 4.3 - - + +
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Residues in contact with PHE 67 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64n LYS* 3.7 22.9 - - + -
65n ARG 4.3 1.8 - - - -
66n LEU* 1.3 79.0 - - - +
68n ASN* 1.3 69.7 + - - +
69n VAL* 3.6 0.7 - - + +
74n GLY* 3.4 5.4 - - - -
75n MET* 2.7 47.6 + - + -
77n VAL* 3.8 40.6 - - + -
81n LEU* 5.4 2.2 - - + -
84n ALA* 4.6 6.1 - - + -
85n ARG* 4.0 35.0 - - + -
88n ALA* 4.1 23.3 - - + -
92n ARG* 5.4 8.7 - - - -
224n HIS* 3.9 5.0 - - - -
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Residues in contact with ASN 68 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66n LEU 5.7 0.8 + - - -
67n PHE* 1.3 77.1 - - - +
69n VAL* 1.3 62.0 + - - +
70n ASP 4.7 2.2 - - - +
73n VAL 4.0 2.9 - - - -
92n ARG* 2.9 28.2 + - - +
224n HIS* 2.6 45.8 + - - +
225n GLU* 5.2 0.9 - - - -
75u GLU 4.7 2.8 + - - -
76u LEU* 3.1 43.9 + - + +
77u LEU 5.0 4.0 + - - -
78u GLY* 5.2 3.0 - - - +
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Residues in contact with VAL 69 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67n PHE* 3.6 2.8 + - + -
68n ASN* 1.3 74.9 - - - +
70n ASP* 1.3 65.1 + - + +
73n VAL* 2.9 16.8 + - + +
75n MET* 3.7 40.8 - - + -
88n ALA* 4.6 4.9 - - - +
91n ALA* 3.8 32.1 - - + +
92n ARG* 3.3 15.3 - - - +
95n ALA* 4.6 1.6 - - + +
111n LEU* 3.7 29.2 - - + -
137n LEU* 4.2 5.8 - - + -
76u LEU* 2.8 17.6 - - - +
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Residues in contact with ASP 70 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68n ASN* 4.5 2.6 - - - +
69n VAL* 1.3 79.4 + - + +
71n ARG* 1.3 76.9 + - - +
72n HIS* 2.9 35.8 + - + +
73n VAL* 2.9 24.2 + - + +
95n ALA* 3.4 27.4 - - + +
99n ARG* 3.0 37.9 + - - -
106n ILE* 4.2 2.6 + - - +
224n HIS* 4.7 3.3 - - - +
72u ILE* 4.0 9.0 - - - +
76u LEU* 3.3 14.5 - - - +
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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