Contacts of the strand formed by residues 312 - 316 (chain A) in PDB entry 5WN0
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 ILE 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 3.3 2.4 - - - -
66A SER* 3.0 44.2 + - - +
265A THR* 3.6 28.5 - - + -
283A ASP* 3.6 24.9 - - + +
284A TYR 3.5 27.8 - - - +
285A PHE* 3.3 28.4 - - + -
298A SER* 5.9 0.2 - - - +
299A LYS 3.3 16.2 - - - +
300A ILE* 4.3 6.1 - - + -
301A ARG* 4.7 0.9 - - - +
310A CYS 4.6 0.4 - - - +
311A PRO* 1.3 79.2 - - - +
313A THR* 1.3 67.7 + - - +
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Residues in contact with THR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 3.8 30.3 - - + -
64A ILE 3.4 6.7 - - - +
65A CYS* 3.7 12.0 - - + +
87A GLU* 2.7 30.2 + - - +
285A PHE* 3.6 3.9 - - - -
297A ASP 3.9 0.2 - - - +
298A SER* 3.4 2.4 - - - -
299A LYS* 2.7 41.6 + - - +
301A ARG* 3.8 19.6 + - - +
312A ILE* 1.3 79.0 + - - +
314A LEU* 1.3 63.2 + - - +
315A TYR* 4.2 8.7 - - + -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU 3.8 0.5 - - - +
63A LYS* 3.3 9.2 - - - +
64A ILE* 2.8 41.7 + - + +
206A VAL* 4.0 15.3 - - + -
252A SER* 4.2 9.0 - - - +
285A PHE* 3.6 45.1 - - + -
287A LEU* 4.3 6.1 - - + -
295A LEU* 3.6 30.7 - - + -
297A ASP 3.4 4.9 - - - +
298A SER* 4.5 1.1 - - - -
313A THR* 1.3 74.6 - - - +
315A TYR* 1.3 62.3 + - - +
316A LEU* 3.7 33.7 - - + -
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Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 2.9 37.8 + - + -
51A GLN 4.3 4.9 - - - +
52A LYS* 3.9 27.5 - - + -
60A ALA* 4.1 15.9 - - + -
62A LEU 3.5 2.7 - - - -
63A LYS* 3.3 51.6 + - + -
295A LEU* 4.1 0.2 - - - +
296A CYS* 2.8 36.0 + - + -
297A ASP* 2.8 38.5 + - + +
299A LYS* 4.0 12.8 - - + -
301A ARG* 3.4 3.0 + - - -
313A THR* 4.2 3.1 - - + -
314A LEU* 1.3 73.2 - - - +
316A LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 3.2 6.7 - - - +
61A THR 2.9 21.1 + - - -
62A LEU* 2.9 38.3 + - + +
165A PHE* 5.9 0.4 - - + -
206A VAL* 4.4 18.4 - - + -
287A LEU* 4.7 8.5 - - + -
291A LEU* 4.5 15.9 - - + +
294A ALA* 3.4 7.9 - - + +
295A LEU* 3.6 23.8 - - + +
296A CYS* 4.0 0.7 - - - -
314A LEU* 3.7 36.8 - - + -
315A TYR* 1.3 82.3 - - - +
317A ALA* 1.3 60.3 + - - +
318A LEU* 4.1 17.5 - - + -
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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