Contacts of the helix formed by residues 112 - 118 (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 PHE 112 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L GLY* 3.5 23.8 - - - -
38L ILE* 3.4 32.1 - - + -
61L VAL* 4.3 18.2 - - + -
87L LEU* 4.6 11.7 - - + -
92L GLU 4.9 3.1 - - - -
94L PRO* 6.2 3.6 - - + -
106L GLU 5.4 0.2 - - - -
107L LEU* 3.1 35.1 - - + +
109L SER* 3.5 15.6 + - - -
111L LYS* 1.3 104.8 - - + +
113L MET* 1.3 54.0 + - - +
114L LYS* 3.1 3.8 - - - -
115L ILE* 2.8 55.4 + - + +
116L ILE 3.7 1.9 + - - -
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Residues in contact with MET 113 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108L ARG* 4.4 28.3 - - - +
109L SER 3.4 16.2 + - - +
110L GLU* 4.2 11.4 + - - +
111L LYS 3.4 2.6 + - - -
112L PHE* 1.3 76.7 - - - +
114L LYS* 1.3 63.0 + - - +
116L ILE* 3.4 28.0 + - + +
117L SER* 3.0 41.9 + - - +
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Residues in contact with LYS 114 (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 GLN* 4.9 11.9 - - - +
94L PRO* 4.0 39.3 - - + -
96L GLY 4.3 6.7 - - - -
97L THR* 4.3 18.0 + - - +
111L LYS 5.0 0.8 + - - +
112L PHE 2.8 5.7 + - - +
113L MET* 1.3 74.1 - - - +
115L ILE* 1.3 62.6 + - - +
117L SER* 3.2 8.1 + - - -
118L LEU* 2.9 52.6 + - + +
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Residues in contact with ILE 115 (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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61L VAL* 3.6 33.0 - - + -
63L VAL* 4.8 7.0 - - + -
85L VAL* 3.8 16.8 - - + -
87L LEU* 4.9 1.1 - - + -
94L PRO* 3.9 23.1 - - + -
99L ILE* 3.7 28.3 - - + +
103L VAL* 4.9 4.0 - - + -
107L LEU* 4.3 21.1 - - + -
112L PHE* 2.8 33.2 + - + +
114L LYS* 1.3 72.5 - - - +
116L ILE* 1.3 59.6 + - + +
118L LEU* 3.0 19.4 + - - +
119L ALA* 3.3 10.6 + - - +
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Residues in contact with ILE 116 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103L VAL* 4.8 2.7 - - + -
104L THR 4.5 6.5 - - - +
105L ARG* 6.2 0.7 - - - -
107L LEU* 3.5 43.3 - - + +
108L ARG* 3.6 47.6 - - + +
112L PHE 3.7 4.2 + - - +
113L MET* 3.4 26.1 + - + +
115L ILE* 1.3 75.6 - - + +
117L SER* 1.3 63.0 + - - +
119L ALA* 3.8 13.2 + - - +
122L VAL* 3.8 32.5 - - + +
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Residues in contact with SER 117 (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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113L MET* 3.0 40.0 + - - +
114L LYS* 3.5 7.9 - - - -
116L ILE* 1.3 79.8 - - - +
118L LEU* 1.3 61.4 + - - +
119L ALA 3.4 2.9 + - - +
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Residues in contact with LEU 118 (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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94L PRO* 5.9 1.1 - - + -
96L GLY 5.0 1.8 - - - +
97L THR 3.2 34.1 - - - +
98L ARG* 4.3 3.8 - - + +
99L ILE* 3.5 31.3 + - + +
114L LYS* 2.9 50.5 + - + +
115L ILE* 3.0 6.8 + - - +
117L SER* 1.3 80.5 - - - +
119L ALA* 1.3 60.6 + - - +
120L PRO* 3.7 3.3 - - - +
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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