Contacts of the strand formed by residues 338 - 345 (chain B) 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 ALA 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU* 4.5 2.5 - - + -
205B LEU 3.3 12.3 - - - +
206B VAL* 4.2 4.7 - - + -
337B GLY* 1.3 71.6 - - - -
339B THR* 1.3 64.8 + - - +
360B HIS* 3.7 3.6 - - - +
361B ILE* 2.9 32.9 + - + +
450B TYR* 2.9 19.6 + - + +
451B PHE* 4.4 1.3 - - + -
454B ILE* 3.9 35.9 - - + -
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 3.8 11.6 - - + +
186B LYS* 2.8 24.7 + - - -
203B VAL 3.7 0.2 - - - +
204B LEU* 3.7 2.4 - - - +
205B LEU* 2.9 41.2 + - - +
338B ALA* 1.3 72.1 - - - +
340B VAL* 1.3 70.8 + - - +
341B VAL* 4.2 9.9 - - + -
358B VAL* 3.8 20.2 - - + -
359B ASP 3.4 12.8 - - - +
360B HIS* 3.0 29.0 + - + +
361B ILE* 4.5 0.7 - - - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 4.4 12.1 - - + -
203B VAL 3.3 4.9 - - - +
204B LEU* 4.1 9.2 - - + -
339B THR* 1.3 77.4 - - - +
341B VAL* 1.3 63.8 + - - +
357B LEU 3.5 3.5 - - - +
359B ASP* 2.7 42.1 + - + +
361B ILE* 3.7 22.4 - - + -
457B MET* 3.3 36.8 - - + -
464B VAL* 5.3 1.1 - - + -
466B ILE* 4.5 2.2 - - + -
489B ILE* 4.3 14.8 - - + -
491B TYR* 3.9 18.3 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 6.3 0.4 - - + -
177B PRO* 5.8 1.3 - - + -
180B TRP* 6.3 0.2 - - + -
183B ILE* 3.9 12.6 - - + -
202B PHE* 3.4 2.0 - - - -
203B VAL* 2.8 51.4 + - + +
205B LEU* 3.8 24.2 - - + -
339B THR* 4.2 4.0 - - + -
340B VAL* 1.3 78.1 - - - +
342B SER* 1.3 71.5 + - - +
343B PHE* 3.8 1.0 + - + -
355B PHE* 4.1 26.0 - - + -
356B GLY 5.1 0.7 - - - +
357B LEU 3.2 9.2 - - - +
358B VAL* 3.7 24.7 - - + -
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 5.5 0.2 + - - -
200B LEU* 4.6 6.7 - - - -
201B TYR 3.4 6.3 - - - -
202B PHE* 3.5 28.7 - - - -
340B VAL 4.1 0.8 + - - -
341B VAL* 1.3 77.4 - - - +
343B PHE* 1.3 60.0 + - - +
344B TYR* 5.1 3.6 + - - -
356B GLY* 2.8 28.0 + - - -
357B LEU* 2.7 42.2 + - - +
491B TYR* 4.1 10.7 + - - -
495B PHE* 4.9 3.8 + - - +
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Residues in contact with PHE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.6 30.3 - + - -
130B ILE* 3.8 18.8 - - + -
143B ILE* 4.1 11.2 - - + -
191B VAL* 4.1 4.5 - - + -
199B ASN 3.6 1.4 - - - +
200B LEU* 3.7 4.3 - - - +
201B TYR* 2.9 61.0 + - + +
202B PHE 4.0 5.6 - - - -
203B VAL* 3.6 27.4 - - + -
341B VAL* 3.9 11.7 - - + -
342B SER* 1.3 74.8 - - - +
344B TYR* 1.3 77.3 + - - +
345B ASP* 4.4 3.6 - - + -
353B THR* 4.2 9.6 - - + -
354B ALA 3.5 11.0 - - - +
355B PHE* 4.2 18.8 - + + -
356B GLY 4.2 0.2 - - - +
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Residues in contact with TYR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 3.4 32.3 - - + -
156B ARG* 3.3 21.2 + - - -
162B PRO* 3.8 22.7 - - + +
170B PHE* 3.6 32.3 - + + -
198B PRO 4.9 3.4 - - - -
199B ASN* 3.1 17.3 - - + -
200B LEU* 3.6 37.7 - - + +
342B SER* 5.1 3.3 + - - -
343B PHE* 1.3 78.9 - - - +
345B ASP* 1.3 65.0 + - - +
353B THR* 3.4 9.5 - - - +
354B ALA* 2.7 38.2 + - + +
355B PHE 4.1 2.5 - - - -
356B GLY* 4.1 14.6 - - - -
494B ASN 4.2 3.3 + - - -
495B PHE* 4.1 5.7 - - - +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 3.3 23.9 - - + -
132B ARG* 2.8 26.7 + - - -
141B TYR* 2.7 35.9 + - - -
143B ILE* 4.1 0.3 - - - +
170B PHE* 3.5 2.9 - - - -
199B ASN* 2.8 34.5 + - - +
201B TYR* 3.5 24.9 + - + -
343B PHE* 4.4 3.1 - - + -
344B TYR* 1.3 75.7 - - - +
346B ALA* 1.3 55.8 + - - +
347B PRO* 3.7 3.8 - - - +
352B HIS 3.1 5.2 - - - -
353B THR* 3.6 5.2 + - - -
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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