Contacts of the strand formed by residues 105 - 111 (chain C) in PDB entry 5DG4
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 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C TYR* 4.8 1.9 + - - -
95C CYS 3.1 15.7 - - - -
97C GLN* 3.7 14.3 - - - +
104C ARG* 1.3 76.9 - - - +
106C TRP* 1.3 69.3 + - - +
119C LEU* 3.6 3.6 - - - +
120C THR* 2.9 34.7 + - - +
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Residues in contact with TRP 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 5.8 0.7 - - - -
62C VAL* 6.1 3.4 - - + -
64C PHE* 4.1 15.9 - + - -
86C VAL* 4.0 13.7 - - + -
93C LEU* 3.7 40.4 - - + -
94C VAL* 4.2 0.5 - - - +
95C CYS* 2.8 67.2 + - + +
97C GLN* 4.7 12.3 - - - +
105C GLY* 1.3 78.0 - - - +
107C LYS* 1.3 71.1 + - - +
108C GLN* 3.8 18.8 - - + -
117C LEU* 3.8 24.5 - - + -
118C GLU 3.1 13.9 - - - +
119C LEU* 4.0 18.6 - - + -
120C THR* 4.6 2.7 - - - +
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Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLU* 4.9 8.0 + - - -
92C VAL* 3.8 18.6 - - + -
93C LEU 3.2 5.6 - - - -
94C VAL* 4.1 25.8 - - + -
106C TRP* 1.3 81.2 - - - +
108C GLN* 1.3 60.5 + - - +
109C TRP* 3.7 15.6 - - + -
117C LEU* 3.4 2.9 - - - +
118C GLU* 2.8 39.3 + - + +
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLN* 2.8 31.7 + - - +
40C LYS* 3.9 15.3 + - - +
42C ILE* 3.6 18.0 - - - +
49C PHE* 5.2 2.2 - - - -
51C THR* 5.8 2.0 - - - +
64C PHE* 6.1 0.2 - - - -
92C VAL* 4.2 0.2 - - - +
93C LEU* 2.8 40.8 + - + +
106C TRP* 3.8 20.1 - - + -
107C LYS* 1.3 76.2 - - - +
109C TRP* 1.3 65.5 + - - +
115C LEU* 3.8 26.1 - - + +
116C TYR 3.2 11.7 - - - +
117C LEU* 3.7 18.0 - - + +
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLN* 3.7 7.2 - - - +
91C ASP* 3.8 20.0 - - - +
92C VAL* 4.1 23.8 - - + -
107C LYS* 3.7 26.2 - - + -
108C GLN* 1.3 84.2 - - - +
110C ILE* 1.3 68.1 + - - +
111C GLU* 2.5 46.9 + - + +
115C LEU* 3.6 2.2 - - - +
116C TYR* 2.8 58.4 + + + +
118C GLU* 3.6 36.6 - - + -
127C ARG* 4.6 6.5 - - - -
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Residues in contact with ILE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C THR* 3.9 32.4 + - + +
3C ASP 3.8 16.6 - - - +
4C GLN* 4.0 23.7 - - + +
8C TRP* 3.7 36.6 - - + -
91C ASP* 4.4 12.8 + - - +
109C TRP* 1.3 78.5 - - - +
111C GLU* 1.3 68.1 + - - +
112C GLY 3.4 22.6 + - - +
114C LYS 3.3 9.0 - - - +
115C LEU* 4.0 11.2 - - + -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 2.5 44.0 + - + +
110C ILE* 1.3 71.7 - - - +
112C GLY* 1.3 65.9 + - - +
113C ASP* 3.1 1.4 + - - +
114C LYS* 3.0 27.8 + - - +
116C TYR* 3.5 29.9 + - + +
127C ARG* 4.6 3.8 + - - -
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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