Contacts of the strand formed by residues 109 - 114 (chain C) in PDB entry 3DC1
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 MET 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A TRP* 6.4 0.4 - - + -
88C LYS* 4.5 28.5 - - + -
91C GLN* 4.3 10.8 - - - -
92C ILE* 5.0 7.2 - - + -
97C PRO* 3.9 26.2 - - + -
99C THR* 3.4 25.4 + - - +
100C ILE* 4.2 24.6 - - + +
107C GLY 3.3 3.1 + - - -
108C GLN* 1.3 81.3 - - - +
110C ASP* 1.3 62.9 + - - +
111C LEU* 5.4 0.2 - - + -
247C LEU* 4.8 4.5 - - + -
275C THR* 3.7 30.3 - - + -
276C GLY* 3.9 6.5 - - - +
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Residues in contact with ASP 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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88C LYS* 3.8 15.5 + - - +
108C GLN 3.1 1.1 + - - +
109C MET* 1.3 77.2 - - - +
111C LEU* 1.3 72.6 + - - +
274C LEU 3.8 0.2 - - - +
275C THR* 3.2 9.9 - - - +
276C GLY 2.6 40.1 + - - +
278C LYS* 3.3 46.0 - - + +
281C ILE* 3.7 24.1 - - + +
282C GLU* 5.0 0.9 + - - +
285C ILE* 4.8 5.9 - - - +
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Residues in contact with LEU 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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78C ALA* 4.7 3.3 - - - +
84C LEU* 3.5 29.5 - - + +
87C LEU* 3.7 49.1 - - + +
88C LYS* 3.8 21.4 - - + +
91C GLN* 3.8 7.6 - - + -
110C ASP* 1.3 86.5 + - - +
112C CYS* 1.3 76.7 + - - +
113C VAL 3.9 1.6 - - - +
273C PHE* 3.8 18.8 - - + -
274C LEU 3.0 13.7 - - - +
275C THR* 3.5 18.2 - - + +
281C ILE* 4.4 3.9 - - - +
285C ILE* 5.2 0.7 - - - +
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Residues in contact with CYS 112 (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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78C ALA* 3.3 26.5 - - + +
111C LEU* 1.3 78.7 - - - +
113C VAL* 1.3 66.8 + - - +
114C THR* 3.4 11.7 + - - +
273C PHE* 3.4 1.2 - - - -
274C LEU* 3.0 47.9 + - - -
281C ILE* 3.5 20.0 - - - -
284C VAL* 4.8 6.7 - - - -
285C ILE* 4.1 13.2 - - + -
288C ILE* 5.2 3.1 - - + -
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Residues in contact with VAL 113 (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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77C SER 4.5 1.6 - - - +
78C ALA* 2.6 24.4 + - - +
79C GLY* 3.8 15.0 - - - -
83C LEU* 3.7 35.4 - - + -
84C LEU* 4.1 9.9 - - + -
87C LEU* 3.8 14.6 - - + -
111C LEU* 3.9 0.6 - - - +
112C CYS* 1.3 75.9 - - - +
114C THR* 1.4 65.1 + - - +
271C ILE* 3.9 15.5 - - + -
272C GLY 3.6 10.8 - - - +
273C PHE* 4.2 1.8 - - - -
288C ILE* 4.7 4.5 - - - +
295C PRO* 3.4 27.2 - - + +
300C GLN* 3.9 8.3 - - + +
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Residues in contact with THR 114 (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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112C CYS* 3.4 23.5 + - - +
113C VAL* 1.4 80.8 - - - +
115C SER* 1.3 59.5 + - - +
116C GLY 2.8 24.8 + - - -
117C SER* 4.0 4.0 - - - -
119C GLN* 3.8 8.3 - - - -
120C GLY* 3.8 27.4 + - - +
270C ARG 3.8 0.3 - - - +
271C ILE* 3.5 5.9 - - - -
272C GLY 2.6 35.3 + - - +
273C PHE* 3.5 4.9 + - - -
274C LEU* 4.4 4.9 - - + -
284C VAL* 5.1 0.2 - - + -
288C ILE* 4.2 13.5 - - + -
295C PRO* 4.0 6.8 - - - +
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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