Contacts of the strand formed by residues 262 - 267 (chain C) in PDB entry 5DO7
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 LYS 262 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C TYR* 3.1 39.2 + - - +
76C VAL* 4.9 1.1 - - + -
80C GLN* 4.1 18.6 - - + +
81C ILE 2.8 15.0 + - - +
82C MET* 3.1 21.9 - - + +
83C CYS* 2.8 31.3 + - - -
260C PHE* 3.3 2.0 - - - -
261C ASP* 1.3 80.7 - - + +
263C ILE* 1.3 54.2 + - - +
274C CYS* 3.9 21.1 - - - -
275C GLY* 3.4 16.4 - - - +
276C THR* 4.8 0.7 - - - +
279C GLU* 5.5 2.0 - - - -
337C LYS* 5.5 5.1 - - - +
338C THR* 3.3 34.7 - - - +
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Residues in contact with ILE 263 (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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83C CYS* 3.3 22.7 - - + +
85C LEU* 4.7 9.9 - - + -
257C PHE* 4.0 8.5 - - + -
260C PHE* 4.7 10.6 + - + +
261C ASP 4.3 0.2 - - - -
262C LYS* 1.3 71.6 - - - +
264C ALA* 1.3 62.9 + - - +
265C ILE* 4.9 7.0 - - + -
273C PHE* 3.9 3.4 - - + -
274C CYS* 3.3 1.6 - - - -
275C GLY 2.8 46.0 + - - +
277C PRO* 4.4 16.4 - - + -
280C MET* 4.0 38.6 - - + -
298C PHE* 3.7 33.4 - - + -
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Residues in contact with ALA 264 (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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74C LEU* 4.2 7.0 - - + -
82C MET* 4.0 22.7 - - + -
83C CYS 2.8 9.7 + - - -
84C ILE* 3.5 12.6 - - + +
85C LEU 3.3 20.6 + - - -
263C ILE* 1.3 76.5 - - - +
265C ILE* 1.3 63.2 + - - +
266C LEU* 5.3 2.2 - - + -
271C LEU* 5.1 2.9 - - + -
273C PHE 3.0 13.9 - - - +
274C CYS* 3.6 18.4 - - + -
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Residues in contact with ILE 265 (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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85C LEU* 3.6 41.3 - - + +
86C GLY* 5.7 0.2 - - - -
87C SER* 5.3 1.3 - - - +
263C ILE* 4.9 5.8 - - + -
264C ALA* 1.3 76.2 - - - +
266C LEU* 1.3 76.5 + - - +
271C LEU* 3.9 1.2 - - - +
272C ILE* 2.8 42.5 + - + -
273C PHE* 2.8 17.6 + - + +
280C MET* 4.7 22.4 - - + -
284C PHE* 5.1 0.9 - - + -
301C TYR* 5.8 1.6 - - + -
302C MET* 4.8 6.5 - - + +
305C THR* 3.6 43.1 - - + +
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Residues in contact with LEU 266 (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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69C LEU* 4.3 8.3 - - + -
72C VAL* 4.7 8.7 - - + -
74C LEU* 6.1 1.6 - - + -
84C ILE* 4.9 9.9 - - + -
85C LEU 3.4 9.1 + - - +
86C GLY* 3.9 2.3 - - - -
87C SER* 3.3 26.9 + - - -
89C GLY 5.4 1.3 - - - +
91C GLY* 3.7 30.1 - - - +
92C LYS* 3.8 11.0 - - - +
95C LEU* 3.5 30.5 - - + -
264C ALA* 5.1 2.0 - - + +
265C ILE* 1.3 87.7 - - - +
267C SER* 1.3 59.3 + - - +
268C PHE 4.2 0.4 - - - -
269C GLY 4.2 8.3 - - - +
270C GLU 3.5 8.1 - - - +
271C LEU* 4.0 24.7 - - + -
272C ILE* 4.9 0.2 - - - -
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Residues in contact with SER 267 (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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87C SER* 4.0 11.2 + - - -
265C ILE 4.5 0.2 + - - -
266C LEU* 1.3 74.1 - - - +
268C PHE* 1.3 82.9 + - - +
270C GLU* 2.8 36.0 + - - +
272C ILE* 3.9 22.6 - - - +
305C THR* 3.9 14.1 + - - -
306C SER* 4.3 3.6 - - - -
307C VAL* 4.7 1.9 + - - +
322C VAL* 4.3 9.7 - - - +
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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