Contacts of the strand formed by residues 65 - 72 (chain X) in PDB entry 5GAG
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 GLY 65 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30X SER* 3.3 1.0 - - - -
31X VAL* 2.9 40.0 + - - +
63X ALA 3.8 1.6 + - - -
64X ASP* 1.3 75.5 - - - +
66X LYS* 1.3 62.1 + - - -
82X ILE* 4.0 6.2 - - - +
83X GLU 3.1 10.3 - - - -
85X GLU* 3.2 25.2 + - - -
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Residues in contact with LYS 66 (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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28X GLY* 4.3 13.6 + - - +
29X GLU 3.1 7.6 - - - +
30X SER* 3.7 20.4 - - - +
65X GLY* 1.3 73.1 - - - -
67X VAL* 1.3 65.6 + - - +
68X LYS 3.7 0.2 + - - -
82X ILE* 3.5 4.5 - - - +
83X GLU* 2.9 48.0 + - + +
85X GLU* 3.9 28.3 - - + +
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Residues in contact with VAL 67 (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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25X ARG* 4.6 6.7 - - + +
26X PHE 3.6 17.0 - - - +
27X GLY* 3.8 2.6 - - - -
28X GLY* 3.3 19.8 + - - -
29X GLU* 3.0 14.7 + - + +
31X VAL* 4.1 23.8 - - + -
37X ILE* 4.3 13.0 - - + -
66X LYS* 1.3 74.8 - - - +
68X LYS* 1.3 65.2 + - - +
69X PHE* 3.9 28.7 - - + -
80X ILE* 4.3 17.7 - - + -
81X SER 4.4 0.4 - - - +
82X ILE* 3.6 17.5 - - + -
83X GLU* 5.8 0.2 - - - -
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Residues in contact with LYS 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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27X GLY* 5.4 0.2 - - - -
67X VAL* 1.3 78.1 - - - +
69X PHE* 1.3 76.8 + - - +
70X GLU* 3.4 27.7 + - - +
79X PHE 3.6 0.3 - - - +
80X ILE* 3.4 5.2 - - - +
81X SER* 2.9 48.8 + - - +
83X GLU* 3.3 35.7 - - + +
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Residues in contact with PHE 69 (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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856A G 3.3 33.5 + - - +
857A G 3.6 43.5 - - - +
23X VAL* 4.1 13.0 - - + -
25X ARG 4.0 15.3 - - - -
26X PHE* 3.8 4.3 - - - -
27X GLY* 3.4 21.5 - - - -
45X PHE* 3.9 15.7 - + - -
67X VAL* 3.9 10.3 - - + -
68X LYS* 1.3 91.2 + - - +
70X GLU* 1.3 64.4 + - - +
78X LYS* 6.1 0.9 - - + -
79X PHE 3.6 2.7 - - - -
80X ILE* 3.5 34.3 - - + -
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Residues in contact with GLU 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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48X GLY* 5.3 1.2 - - - -
68X LYS* 3.4 25.9 + - - +
69X PHE* 1.3 75.9 - - - +
71X VAL* 1.3 62.5 + - - +
72X LYS* 3.7 33.6 - - + +
78X LYS* 3.4 7.2 - - - +
79X PHE* 2.8 48.6 + - + +
81X SER* 3.4 28.5 + - - -
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Residues in contact with VAL 71 (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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12B C 3.9 21.6 + - - +
70X GLU* 1.3 75.8 - - - +
72X LYS* 1.3 67.2 + - - +
73X GLY 5.7 0.2 - - - +
76X ASN* 3.7 35.9 - - + +
77X ARG 3.3 7.2 - - - +
78X LYS* 4.2 17.0 - - + -
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Residues in contact with LYS 72 (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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11B C 2.8 42.4 + - - +
12B C 4.7 5.2 + - - -
70X GLU* 3.7 34.9 - - + +
71X VAL* 1.3 80.6 + - - +
73X GLY* 1.3 65.5 + - - +
76X ASN* 3.5 1.5 - - - -
77X ARG* 3.0 35.6 + - - +
79X PHE* 4.1 24.9 - - + -
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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