Contacts of the strand formed by residues 321 - 326 (chain A) in PDB entry 6RUT
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 TRP 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.8 2.9 - - + -
135A PRO* 4.0 22.2 - - + +
291A ILE* 4.5 14.1 - - + -
294A LEU* 4.0 22.7 - - + -
295A TYR* 4.1 20.0 - + + -
298A SER* 3.1 32.8 + - - +
312A MET* 5.3 0.2 - - - -
313A GLY 5.1 1.6 + - - -
319A SER* 3.3 10.6 - - - -
320A MET* 1.4 123.3 - - + +
322A TYR* 1.3 65.0 + - - +
323A TRP* 3.2 30.0 - + - -
337A PRO* 3.6 18.8 - - + +
338A THR 3.3 18.6 - - - +
339A TRP* 3.6 27.1 - + + +
340A PHE* 3.6 12.1 - - - -
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Residues in contact with TYR 322 (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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310A VAL* 4.9 3.8 - - + -
311A VAL 3.5 13.0 - - - +
312A MET* 3.8 27.1 - - + +
321A TRP* 1.3 75.8 - - - +
323A TRP* 1.3 65.8 + - - +
324A VAL* 4.0 13.9 - - + -
337A PRO* 3.1 6.6 - - - +
338A THR* 2.8 64.7 + - - +
339A TRP 4.2 0.7 - - - -
340A PHE* 3.5 31.2 - + + -
343A THR* 2.7 31.9 + - - +
552A LEU* 5.8 0.2 - - + -
555A ALA* 3.6 14.7 - - + +
568A VAL* 4.3 0.9 - - - +
570A TRP* 3.4 31.0 - + - -
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Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.6 22.2 - - + +
133A ASP 3.1 28.9 + - - -
134A VAL* 4.8 1.1 - - - -
295A TYR* 3.6 27.6 - + - -
298A SER* 3.5 20.0 - - - -
299A THR* 3.5 17.3 - - + -
309A ILE 4.3 0.2 - - - -
310A VAL* 3.2 11.5 - - - +
311A VAL* 2.8 60.7 + - + -
321A TRP* 3.2 25.6 - + - -
322A TYR* 1.3 76.0 - - - +
324A VAL* 1.3 61.7 + - - +
325A VAL* 4.1 9.4 - - + -
335A ASN* 3.2 21.6 + - + -
336A LYS 3.5 4.3 - - - -
337A PRO* 3.2 30.8 - - + -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A HIS* 3.4 35.4 - - + -
309A ILE 3.6 3.6 - - - +
310A VAL* 4.5 2.7 - - + -
322A TYR* 4.0 15.4 + - + -
323A TRP* 1.3 77.1 - - - +
325A VAL* 1.3 62.9 + - - +
336A LYS 4.5 5.5 + - - +
338A THR* 4.8 3.9 + - - +
552A LEU* 3.5 34.3 - - + +
555A ALA* 4.0 24.0 - - + -
556A LYS* 3.2 39.9 + - + +
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Residues in contact with VAL 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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111A VAL* 6.0 0.2 - - + -
130A TYR* 3.5 37.5 - - + -
132A LEU* 4.0 22.4 - - + -
308A HIS* 3.3 6.4 - - - -
309A ILE* 2.8 52.2 + - + +
311A VAL* 5.8 0.7 - - + -
323A TRP* 4.4 8.5 - - + -
324A VAL* 1.3 78.3 - - - +
326A GLU* 1.3 68.0 + - - +
327A ARG 3.5 0.2 + - - -
335A ASN* 3.7 31.9 - - + +
556A LYS* 4.7 2.0 - - - +
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Residues in contact with GLU 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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130A TYR* 3.8 0.3 - - - -
307A ASN* 3.6 12.8 - - - +
308A HIS* 2.9 41.8 + - - -
324A VAL* 4.1 1.6 + - - +
325A VAL* 1.3 76.9 - - - +
327A ARG* 1.3 66.0 + - - +
328A SER* 3.5 20.4 - - - +
329A ALA* 3.2 26.6 + - + +
335A ASN* 5.0 0.4 + - - -
553A ARG* 4.0 16.3 + - - +
556A LYS* 4.3 25.8 - - + +
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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