Contacts of the strand formed by residues 664 - 670 (chain B) in PDB entry 4CEJ
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 ARG 664 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LEU* 3.9 1.8 - - - +
310B GLU* 3.6 34.9 + - - +
311B ALA* 3.2 16.3 - - + +
330B GLU* 4.5 5.5 + - - -
334B LEU* 3.8 18.8 - - - +
338B LYS* 3.8 32.1 - - - +
340B TYR* 3.8 20.7 + - - +
602B SER 3.0 2.8 + - - -
603B CYS* 3.4 10.1 - - - -
604B THR 3.1 23.7 + - - -
661B PRO* 3.2 10.9 - - - +
663B ASP* 1.3 85.7 - - + +
665B LEU* 1.3 60.1 + - - +
666B TYR* 3.3 31.2 + - + -
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Residues in contact with LEU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.9 13.2 - - + +
293B LEU* 3.7 22.7 - - + -
311B ALA 2.8 10.0 + - - +
312B LEU* 3.3 14.7 - - + +
313B THR 3.0 24.1 + - - -
604B THR* 3.4 37.2 - - + +
606B VAL* 4.3 6.7 - - + -
657B ALA 4.0 5.6 - - - +
658B PHE* 3.2 38.4 - - + +
661B PRO* 3.8 11.4 - - + -
664B ARG* 1.3 75.1 - - - +
666B TYR* 1.3 73.0 + - - +
667B VAL* 4.4 4.0 - - + -
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Residues in contact with TYR 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA 5.5 0.9 - - - -
313B THR* 3.2 23.1 - - - +
315B MET* 3.7 23.3 - - + -
330B GLU* 2.4 47.0 + - + +
334B LEU* 3.8 11.0 - - + +
603B CYS* 4.9 2.0 - - + -
604B THR 2.8 17.9 + - - +
605B PHE* 3.4 44.2 - + + -
606B VAL* 2.8 27.4 + - - +
664B ARG* 3.3 41.7 + - + -
665B LEU* 1.3 78.9 - - - +
667B VAL* 1.3 64.9 + - - +
668B SER* 4.0 1.1 - - - +
698B ARG* 4.1 6.1 - - - -
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Residues in contact with VAL 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 5.0 3.4 - - + -
313B THR 2.9 9.7 + - - -
314B VAL* 3.3 13.8 - - + +
315B MET* 2.9 23.0 + - - +
606B VAL* 3.6 8.3 - - + +
609B ALA* 4.0 23.8 - - + -
614B LEU* 6.3 0.2 - - + -
658B PHE* 3.5 39.5 - - + -
665B LEU* 4.4 9.6 - - + -
666B TYR* 1.3 78.3 - - - +
668B SER* 1.3 61.1 + - - +
669B TYR* 4.7 0.7 - - - -
684B ILE* 5.3 1.6 - - + -
685B VAL* 5.0 8.3 - - + -
688B LEU* 4.0 25.1 - - + -
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Residues in contact with SER 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 3.1 32.7 - - - +
317B ALA* 5.8 0.2 - - - -
323B GLU* 3.0 31.9 + - - +
327B ILE* 4.0 4.0 - - - +
605B PHE* 5.3 0.9 - - - +
606B VAL 2.9 16.4 + - - +
607B LEU* 3.8 8.7 - - - +
608B GLY 3.3 6.4 + - - -
609B ALA* 3.0 24.9 + - - +
666B TYR 5.2 0.2 + - - -
667B VAL* 1.3 74.2 - - - +
669B TYR* 1.3 62.8 + - - +
700B LEU* 4.4 2.0 - - - -
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Residues in contact with TYR 669 (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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314B VAL* 4.2 3.4 - - + -
315B MET 3.1 16.7 + - - -
316B GLN* 2.6 39.8 + - + -
317B ALA* 2.9 23.1 + - - +
323B GLU* 4.4 1.8 - - - -
609B ALA* 3.3 26.9 - - + +
610B ASN* 3.9 2.0 - - - +
667B VAL 4.7 2.9 - - - -
668B SER* 1.3 78.3 - - - +
670B PRO* 1.3 77.3 - - + +
671B ILE* 4.2 5.8 - - + -
681B PRO* 3.4 39.0 - - + +
685B VAL* 3.9 25.5 - - + +
686B LYS* 5.7 0.3 + - - -
697B GLU* 2.9 24.1 + - - -
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Residues in contact with PRO 670 (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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317B ALA* 3.3 9.0 - - + +
319B ASN* 3.5 32.5 - - - +
320B ARG* 3.8 14.4 - - + +
323B GLU* 3.2 18.4 - - - +
355B TYR* 3.6 10.5 - - - +
608B GLY* 3.8 2.0 - - - -
610B ASN* 2.8 47.5 + - - +
669B TYR* 1.3 89.0 - - - +
671B ILE* 1.3 61.1 + - - +
672B ALA 3.5 4.9 - - - +
679B LEU* 3.4 9.5 - - + +
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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