Contacts of the strand formed by residues 312 - 317 (chain C) in PDB entry 3O4O
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 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C TRP* 3.4 6.2 - - - +
262C THR* 2.4 47.8 + - + +
263C ALA 3.2 8.7 - - - +
264C ASN* 3.2 31.9 + - - +
311C PHE* 1.3 71.6 - - - +
313C CYS* 1.3 61.9 + - - +
314C VAL* 3.5 6.6 + - + +
323C THR* 2.9 43.5 + - - +
324C LEU 2.6 14.6 - - - +
325C ARG* 3.6 31.9 - - + +
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Residues in contact with CYS 313 (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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226C ILE* 4.2 4.7 - - - +
245C CYS* 1.8 53.6 - - + -
259C LEU* 3.4 22.2 - - - -
260C TRP 4.5 0.2 - - - -
261C TRP* 4.2 20.1 - - + +
312C LYS* 1.3 70.5 - - - +
314C VAL* 1.3 60.8 + - - +
315C VAL* 3.7 2.5 + - - -
323C THR* 3.3 5.9 - - - -
324C LEU* 2.8 38.3 + - + +
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 4.5 0.7 - - - +
258C MET 3.6 0.2 - - - +
259C LEU* 3.5 4.6 - - - +
260C TRP* 2.7 88.9 + - + +
262C THR* 4.1 14.6 - - + -
312C LYS* 3.5 3.7 + - + +
313C CYS* 1.3 71.3 - - - +
315C VAL* 1.3 62.9 + - - +
316C HIS* 4.4 4.7 - - + -
321C PHE* 3.8 28.3 - - + -
322C GLN 3.7 11.2 - - - +
323C THR* 4.0 14.6 - - - +
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Residues in contact with VAL 315 (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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224C PRO* 4.2 26.0 - - + -
226C ILE* 3.7 27.1 - - + -
247C VAL* 4.1 22.4 - - + -
257C THR* 5.2 8.1 - - + -
258C MET 3.3 8.3 - - - +
259C LEU* 4.3 6.7 - - + +
313C CYS* 3.7 1.5 + - - +
314C VAL* 1.3 71.5 - - - +
316C HIS* 1.3 69.5 + - - +
317C ASN* 5.3 0.9 - - - +
320C SER* 3.8 3.0 - - - +
322C GLN* 3.0 53.3 + - + +
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Residues in contact with HIS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 5.5 7.2 - - - +
51A GLU* 6.0 3.4 - - + -
52A SER 3.3 24.3 + - - -
53A ASN* 3.9 15.9 - - - -
55A LYS 4.2 1.4 + - - -
56A ILE* 3.0 38.5 - - + +
57A PRO* 5.8 2.5 - - + -
256C THR 3.5 2.3 - - - +
257C THR* 4.8 0.2 - - - -
258C MET* 2.9 43.8 + - + +
314C VAL* 4.4 6.1 - - + -
315C VAL* 1.3 79.8 - - - +
317C ASN* 1.3 76.6 + - - +
320C SER 3.2 16.2 + - - -
321C PHE* 3.5 28.7 - + + -
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Residues in contact with ASN 317 (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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53A ASN 5.0 0.2 - - - +
56A ILE* 4.0 6.5 - - - -
221C GLU* 2.9 31.0 + - - +
222C THR 3.5 13.7 + - - -
224C PRO* 3.9 13.6 - - - +
249C LEU* 5.6 0.2 - - - +
256C THR* 3.8 19.5 - - + -
257C THR* 3.7 22.3 + - - -
315C VAL* 5.3 1.5 - - + +
316C HIS* 1.3 87.2 + - - +
318C THR* 1.3 64.2 + - - +
319C LEU* 2.8 15.4 + - - +
320C SER* 3.0 27.6 + - - +
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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