Contacts of the strand formed by residues 66 - 70 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X PHE* 3.9 15.5 - - + -
49X VAL* 3.6 15.0 - - + -
64X LYS* 4.0 15.9 - - - +
65X ARG* 1.3 90.8 - - - +
67X PHE* 1.3 68.1 + - - +
68X ASN* 5.7 1.0 + - - -
75X MET 3.2 2.7 - - - +
76X ALA* 3.5 25.4 - - + -
212X GLU* 3.7 35.9 + - + +
213X LEU 3.8 12.3 - - - +
214X SER* 3.2 32.8 - - - +
224X HIS* 5.1 4.3 - - + +
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Residues in contact with PHE 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X LYS* 3.7 22.9 - - + -
65X ARG* 4.5 0.2 - - - -
66X LEU* 1.3 79.2 - - - +
68X ASN* 1.3 68.5 + - - +
69X VAL* 3.5 0.8 + - + -
74X GLY* 3.4 6.1 - - - -
75X MET* 2.7 58.6 + - + +
77X VAL* 3.9 36.6 - - + -
81X LEU* 5.1 2.9 - - + -
84X ALA* 4.6 8.7 - - + -
85X ARG* 3.9 34.5 - - + -
88X ALA* 4.1 15.7 - - + -
92X ARG* 5.0 13.9 - - - -
224X HIS* 3.8 4.5 - - - -
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Residues in contact with ASN 68 (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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66X LEU 5.7 1.0 + - - -
67X PHE* 1.3 75.5 - - - +
69X VAL* 1.3 60.5 + - - +
70X ASP 4.6 1.0 - - - +
73X VAL 4.0 4.0 - - - -
92X ARG* 3.0 27.9 + - - +
224X HIS* 2.7 46.6 + - - +
225X GLU* 5.0 1.9 - - - +
75g GLU 5.0 2.6 + - - -
76g LEU* 3.3 47.2 + - + +
77g LEU 5.1 2.8 + - - -
78g GLY* 5.5 2.0 - - - +
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Residues in contact with VAL 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67X PHE* 3.5 3.5 + - + -
68X ASN* 1.3 73.2 - - - +
70X ASP* 1.3 63.2 + - + +
73X VAL* 3.0 18.0 + - + +
75X MET* 3.7 39.7 - - + -
88X ALA* 4.3 7.0 - - - +
91X ALA* 3.7 36.1 - - + +
92X ARG* 3.3 19.9 - - + +
95X ALA* 4.4 2.6 - - + +
111X LEU* 3.8 23.8 - - + -
137X LEU* 4.6 2.0 - - + -
76g LEU* 3.2 11.4 - - - +
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Residues in contact with ASP 70 (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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68X ASN* 4.4 2.3 - - - +
69X VAL* 1.3 78.7 + - + +
71X ARG* 1.3 81.7 + - - +
72X HIS* 2.9 34.8 + - + +
73X VAL* 2.9 25.3 + - + +
95X ALA* 3.4 26.3 - - + +
96X SER 5.6 0.2 - - - -
99X ARG* 3.0 35.7 + - - -
106X ILE* 4.4 1.9 + - - +
224X HIS* 4.6 2.9 - - - +
72g ILE* 3.7 9.7 - - - +
76g LEU* 3.3 13.8 - - - +
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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