Contacts of the strand formed by residues 106 - 112 (chain L) in PDB entry 5G04
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 GLN 106 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1508A GLY* 4.9 6.3 - - - -
1509A PRO* 4.9 15.5 - - - +
1510A HIS* 5.4 3.6 - - - +
97L ARG* 4.1 4.3 - - - -
98L VAL 3.0 29.5 + - - +
104L ASN* 3.6 23.9 + - - +
105L LEU* 1.3 78.3 - - - +
107L GLU* 1.3 69.9 + - - +
108L ILE* 3.5 7.2 + - + +
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Residues in contact with GLU 107 (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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95L SER* 2.9 28.6 + - - +
96L VAL 3.6 8.1 - - - +
97L ARG* 3.8 18.9 + - + +
106L GLN* 1.3 75.4 - - - +
108L ILE* 1.3 63.3 + - - +
109L ARG 4.2 8.3 - - - +
110L GLN* 3.3 37.1 + - - +
142L LEU* 4.6 3.5 - - - +
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Residues in contact with ILE 108 (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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96L VAL* 3.0 21.5 + - + +
97L ARG 4.1 0.4 - - - +
98L VAL* 3.6 44.2 - - + +
106L GLN* 3.7 16.2 - - + +
107L GLU* 1.3 75.7 - - - +
109L ARG* 1.3 65.9 + - + +
124L LEU* 3.6 32.5 - - + -
125L THR* 3.2 36.3 + - - +
126L ASP 5.3 0.4 - - - +
132L THR* 4.9 3.6 - - + +
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Residues in contact with ARG 109 (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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96L VAL* 3.2 30.9 + - + +
107L GLU* 3.8 3.4 - - - +
108L ILE* 1.3 91.1 - - + +
110L GLN* 1.3 66.6 + - - +
111L LEU* 3.4 28.0 - - + +
121L HIS 4.5 3.0 + - - -
122L VAL* 3.4 15.0 - - + +
123L PRO* 3.0 54.1 + - - +
124L LEU* 5.1 0.7 - - + -
125L THR* 3.5 18.6 - - - +
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Residues in contact with GLN 110 (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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93L LYS* 4.3 23.2 - - - +
94L ILE 3.5 11.8 - - - +
95L SER* 4.1 3.4 - - - -
96L VAL* 5.6 0.2 - - - -
107L GLU* 3.3 29.0 + - - +
109L ARG* 1.3 78.6 + - - +
111L LEU* 1.3 72.3 + - - +
112L GLU* 4.3 1.6 + - - +
142L LEU* 3.6 26.5 - - - +
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Residues in contact with LEU 111 (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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79L ILE* 5.7 0.7 - - + -
92L SER 3.9 0.5 - - - +
93L LYS* 3.6 3.8 - - - +
94L ILE* 2.9 50.0 + - + +
96L VAL* 5.4 1.3 - - + -
109L ARG* 3.4 39.3 - - + +
110L GLN* 1.3 82.9 - - - +
112L GLU* 1.3 60.3 + - - +
113L LEU* 3.4 20.5 + - + +
120L ILE* 3.8 19.7 - - + -
121L HIS 4.8 1.6 - - - +
122L VAL* 3.6 34.1 - - + -
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Residues in contact with GLU 112 (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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7L THR* 4.9 2.8 + - - +
92L SER* 3.1 31.4 + - - +
93L LYS* 3.3 27.5 - - + +
110L GLN* 4.3 2.3 + - + +
111L LEU* 1.3 72.6 - - - +
113L LEU* 1.3 68.4 + - - +
114L VAL* 4.2 17.6 + - + +
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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