Contacts of the strand formed by residues 77 - 83 (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 ARG 77 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2332A C 2.9 31.3 + - - -
2333A A 2.8 37.8 + - - -
46X HIS* 3.6 25.4 + - + +
71X VAL* 3.3 3.8 - - - -
72X LYS 3.0 31.5 + - - +
73X GLY* 5.7 1.6 - - - -
74X PRO* 6.3 0.4 - - + -
75X LYS* 3.7 43.4 + - + +
76X ASN* 1.3 75.0 - - - +
78X LYS* 1.3 61.9 - - - +
79X PHE* 3.5 24.7 + - + -
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Residues in contact with LYS 78 (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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857A G 5.6 1.3 - - - +
858A G 2.7 42.8 + - - +
859A G 5.7 2.8 + - - -
44X LYS* 4.0 22.4 + - - +
45X PHE* 3.3 29.3 - - + -
46X HIS* 3.2 22.7 + - - -
69X PHE* 6.1 1.3 - - + -
70X GLU 3.4 4.5 - - - +
71X VAL* 4.2 17.3 - - + -
76X ASN 5.2 3.6 - - - +
77X ARG* 1.3 74.7 - - - +
79X PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 79 (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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2334A U 5.0 12.1 - - - -
45X PHE* 5.3 0.4 - - - -
46X HIS* 3.7 24.0 - + + -
47X ALA 3.5 29.8 - - - -
48X GLY* 4.4 4.5 - - - -
68X LYS 3.6 0.2 - - - +
69X PHE* 3.6 3.7 - - - +
70X GLU* 2.8 56.4 + - + +
72X LYS* 4.1 23.8 - - + -
73X GLY* 5.9 0.9 - - - -
77X ARG* 3.5 38.4 - - + -
78X LYS* 1.3 79.5 - - - +
80X ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 80 (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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37X ILE* 3.7 33.9 - - + -
38X VAL* 4.1 9.9 - - + -
45X PHE* 4.0 13.9 - - + -
46X HIS 3.2 12.1 + - - +
48X GLY* 2.7 30.1 + - - -
51X VAL* 3.5 18.8 - - + +
59X LEU* 3.9 19.7 - - + -
67X VAL* 4.3 7.4 - - + -
68X LYS 3.4 4.9 - - - +
69X PHE* 3.5 38.6 - - + -
78X LYS 4.3 0.4 + - - -
79X PHE* 1.3 71.7 - - - +
81X SER* 1.3 68.0 + - - +
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Residues in contact with SER 81 (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* 3.9 1.3 - - - -
49X ALA* 3.3 32.1 - - - -
51X VAL* 3.9 0.4 - - - -
68X LYS* 2.9 43.9 + - - +
70X GLU* 3.4 22.8 + - - -
79X PHE 3.8 1.4 + - - -
80X ILE* 1.3 75.6 - - - +
82X ILE* 1.3 72.2 + - - +
83X GLU* 5.1 2.3 - - - +
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Residues in contact with ILE 82 (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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31X VAL* 4.4 10.3 - - + -
37X ILE* 4.5 9.9 - - + -
49X ALA* 3.0 20.7 + - - +
50X ASN* 3.6 31.2 + - + +
51X VAL* 3.7 17.0 - - + -
61X ALA* 4.8 2.7 - - + -
63X ALA 4.0 20.4 - - - +
64X ASP 4.0 8.3 - - - +
65X GLY* 4.0 3.6 - - - -
66X LYS 3.5 12.8 - - - +
67X VAL* 3.6 24.2 - - + -
81X SER* 1.3 85.7 + - - +
83X GLU* 1.3 77.1 + - - +
84X ALA 4.0 0.2 + - - -
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Residues in contact with GLU 83 (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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65X GLY* 3.1 2.9 - - - -
66X LYS* 2.9 47.8 + - + +
68X LYS* 3.3 45.5 - - + +
81X SER* 5.1 2.7 - - - +
82X ILE* 1.3 78.8 - - - +
84X ALA* 1.3 68.4 + - - +
85X GLU* 4.1 0.5 - - - -
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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