Contacts of the strand formed by residues 76 - 79 (chain L) 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 VAL 76 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2684A U 3.6 29.6 - - - +
67L LYS 4.8 3.6 - - - +
69L VAL 3.3 12.3 - - - +
70L ARG* 3.7 16.6 - - - -
74L GLY 3.5 10.5 - - - +
75L SER* 1.3 84.0 - - - +
77L ILE* 1.3 67.1 + - - +
78L ARG* 3.9 35.2 + - + +
71Q GLU 3.9 0.2 - - - +
72Q ARG* 3.3 6.8 - - - +
73Q VAL* 2.8 42.7 + - + +
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Residues in contact with ILE 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L THR 4.8 0.3 - - - +
68L GLY* 2.9 21.5 - - - -
69L VAL* 3.2 21.8 + - + +
71L ARG* 3.3 33.7 - - + +
75L SER 5.7 0.4 - - - -
76L VAL* 1.3 79.5 - - - +
78L ARG* 1.3 61.7 + - - +
79L PHE* 3.7 35.3 + - + -
104L THR* 4.6 2.2 - - + -
123L LEU* 3.8 22.4 - - + -
70Q VAL* 4.6 6.5 - - + -
71Q GLU 3.6 7.9 - - - +
72Q ARG* 3.6 34.5 - - + +
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Residues in contact with ARG 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2684A U 3.5 15.8 + - - -
2685A G 3.3 40.9 + - - -
66L LYS 3.8 14.8 - - - +
67L LYS* 3.6 22.2 - - - +
68L GLY* 4.1 3.1 - - - -
76L VAL* 3.9 14.9 + - + +
77L ILE* 1.3 76.4 - - - +
79L PHE* 1.3 72.1 + - - +
60Q THR* 4.4 5.9 + - - +
71Q GLU* 3.0 65.4 + - + +
73Q VAL* 3.8 15.5 - - + +
101Q ARG* 4.7 7.2 - - - +
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Residues in contact with PHE 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L VAL* 5.8 2.5 - - + -
63L VAL 3.9 5.4 - - - -
64L ARG* 3.3 45.5 - - + -
65L THR 3.4 18.3 + - - +
66L LYS* 3.3 25.7 - - - +
68L GLY* 6.3 0.2 - - - -
69L VAL* 6.2 0.2 - - + -
77L ILE* 3.7 29.4 - - + -
78L ARG* 1.3 84.9 - - - +
80L ASP* 1.3 66.8 + - - +
81L GLY 3.4 6.5 - - - +
102L PRO* 4.5 5.8 - - + -
103L VAL 4.8 2.9 - - - -
104L THR* 4.1 17.5 - - + -
123L LEU* 4.2 10.3 - - + -
68Q GLU* 3.6 16.4 - - - +
69Q GLY 3.4 12.6 - - - -
70Q VAL* 3.7 21.1 - - + -
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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