Contacts of the strand formed by residues 319 - 324 (chain B) in PDB entry 6G4N
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 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 4.8 5.4 - - + -
222B ALA* 3.2 24.0 - - + +
224B LEU* 4.4 9.9 - - + -
317B THR* 4.2 2.2 - - + -
318B GLN* 1.3 79.5 - - - +
320B LEU* 1.3 60.8 + - - +
321B LEU* 4.1 20.0 - - + -
407B PHE* 4.1 16.8 - - + -
408B VAL* 4.7 1.6 - - + -
411B TYR* 3.4 54.1 - - + +
417B GLY 2.9 8.0 + - - +
418B THR* 3.9 18.4 - - + +
419B TYR* 3.0 24.3 + - - -
476B PHE* 3.6 6.8 - - - -
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Residues in contact with LEU 320 (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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222B ALA 3.0 5.1 + - - -
223B ILE* 3.0 16.0 - - + +
224B LEU* 2.7 32.2 + - - +
319B ILE* 1.3 73.3 - - - +
321B LEU* 1.3 57.6 + - - +
419B TYR* 3.4 20.0 - - + -
421B TYR* 4.0 2.5 - - + -
472B TYR 5.3 0.2 - - - +
473B TRP* 3.6 42.4 - - + -
476B PHE* 3.6 33.2 - - + -
482B PRO* 3.6 17.0 - - + -
492B TRP* 3.5 27.8 - - + -
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Residues in contact with LEU 321 (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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224B LEU* 2.9 28.3 - - + +
319B ILE* 4.1 14.1 - - + -
320B LEU* 1.3 78.9 - - - +
322B GLY* 1.3 53.0 + - - +
404B LEU* 4.0 22.7 - - + -
407B PHE* 4.0 26.2 - - + -
408B VAL* 3.5 29.4 - - + -
418B THR* 4.0 9.0 - - + -
419B TYR 2.9 17.8 + - - +
420B LEU* 3.2 17.9 - - + -
421B TYR* 2.7 39.1 + - - -
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Residues in contact with GLY 322 (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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224B LEU 3.2 3.6 + - - -
226B SER 2.8 31.2 + - - -
321B LEU* 1.3 80.7 - - - +
323B VAL* 1.3 62.0 + - - +
404B LEU* 3.8 4.6 - - - +
420B LEU* 4.1 7.6 - - - -
421B TYR* 3.0 31.3 + - - -
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Residues in contact with VAL 323 (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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226B SER* 4.0 6.7 - - - -
322B GLY* 1.3 79.7 - - - +
324B ASN* 1.3 63.1 + - - +
327B GLU* 4.2 3.8 - - + +
400B VAL* 3.8 23.1 - - + -
401B ILE* 3.4 36.8 - - + +
404B LEU* 4.0 22.9 - - + -
421B TYR* 3.2 6.5 + - - +
422B PHE* 3.5 21.0 - - + -
423B PHE 2.7 31.4 + - - +
516B LEU* 4.4 8.1 - - + -
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Residues in contact with ASN 324 (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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226B SER* 3.9 0.3 + - - -
323B VAL* 1.3 88.5 - - - +
325B LYS* 1.3 66.7 + - - +
326B ASP 3.3 2.0 + - - -
327B GLU* 3.0 30.7 + - - +
401B ILE* 4.2 5.0 - - - +
421B TYR* 4.5 1.7 - - - -
422B PHE* 4.5 0.9 - - - -
423B PHE* 3.0 27.6 - - - +
438B VAL* 3.5 21.5 - - + +
439B ILE 3.4 17.8 + - - -
440B HIS* 4.2 0.2 - - - +
441B GLY 3.6 5.9 - - - +
443B GLU* 2.9 44.5 + - - +
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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