Contacts of the strand formed by residues 324 - 327 (chain A) in PDB entry 5W6V
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 PRO 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.6 34.8 - - + +
253A ARG* 4.0 13.5 - - + -
256A PHE* 5.8 0.2 - - + -
282A VAL* 3.7 13.7 - - + -
283A THR* 3.3 25.1 - - - +
284A ARG 5.9 0.4 - - - -
285A ARG 3.6 12.8 - - - +
286A PRO* 4.1 0.9 - - + -
287A ALA* 5.0 0.5 - - - +
322A HIS 4.6 1.3 - - - +
323A LEU* 1.3 95.3 - - + +
325A CYS* 1.3 63.2 + - - +
338A PRO* 4.6 0.7 - - - +
339A LEU* 3.3 29.5 + - + +
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Residues in contact with CYS 325 (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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282A VAL* 3.5 5.9 - - - +
283A THR* 2.9 38.8 + - + +
287A ALA* 3.6 37.0 - - - -
290A GLN* 4.6 4.5 - - - -
306A VAL* 4.1 26.5 - - - -
324A PRO* 1.3 75.6 - - - +
326A LEU* 1.3 62.4 + - - +
336A TYR* 3.8 18.8 - - + -
337A LEU 3.4 10.5 - - - +
338A PRO* 4.2 6.5 - - - -
339A LEU* 4.3 2.7 - - - -
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Residues in contact with LEU 326 (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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228A VAL* 4.3 12.3 - - + -
256A PHE* 4.4 2.0 - - + -
260A ILE* 4.0 22.9 - - + -
265A VAL* 4.1 22.0 - - + -
279A VAL* 3.7 33.2 - - + -
281A ASN 3.7 1.8 - - - -
282A VAL* 3.8 23.8 - - + -
325A CYS* 1.3 71.7 - - - +
327A GLN* 1.3 62.0 + - - +
328A VAL* 3.7 7.5 + - + +
336A TYR* 3.2 4.9 - - - -
337A LEU* 2.7 42.0 + - + +
339A LEU* 3.6 23.3 - - + -
342A CYS* 4.4 9.9 - - - -
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Residues in contact with GLN 327 (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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279A VAL* 3.7 1.7 - - - -
280A CYS* 2.9 43.0 + - - -
281A ASN* 2.7 41.5 + - + +
283A THR* 4.9 4.7 + - + +
325A CYS 3.8 2.2 + - - -
326A LEU* 1.3 71.2 - - - +
328A VAL* 1.3 65.2 + - - +
332A GLN* 3.7 26.8 + - - +
333A LYS 3.5 21.8 + - - +
334A HIS* 3.7 15.2 + - - -
335A THR 3.5 6.7 - - - +
336A TYR* 3.6 26.7 - - + -
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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