Contacts of the strand formed by residues 614 - 620 (chain A) in PDB entry 1PJR
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 GLU 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A ILE* 4.1 1.5 - - - +
319A LYS* 2.7 45.8 + - + +
320A PRO 5.5 3.4 - - - +
339A ARG* 2.9 38.9 + - - +
348A GLU* 3.3 5.2 - - - +
349A ARG* 2.7 30.5 + - - +
573A PRO 3.2 3.0 + - - -
574A VAL* 3.4 18.0 - - + +
575A VAL 3.1 23.2 + - - -
611A ALA* 3.7 7.7 - - - +
613A GLU* 1.3 83.3 - - + +
615A LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 615 (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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292A ILE* 4.5 10.1 - - + +
295A ALA* 5.6 0.2 - - + -
320A PRO 4.2 2.8 + - - +
321A ILE* 3.5 39.6 - - + +
322A LEU* 3.3 19.1 + - - +
575A VAL* 3.5 15.3 - - + +
577A LEU* 4.0 20.6 - - + -
608A ILE* 3.9 39.9 - - + +
611A ALA* 4.2 15.0 - - + -
614A GLU* 1.3 75.7 - - - +
616A VAL* 1.3 66.4 + - - +
617A LEU* 3.8 20.2 - - + -
641A ILE* 5.6 1.3 - - + -
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Residues in contact with VAL 616 (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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322A LEU* 3.3 25.1 - - + +
324A TYR 5.5 0.2 - - - +
335A PHE* 4.1 17.9 - - + -
339A ARG* 4.1 17.5 - - - +
574A VAL* 4.3 7.2 - - + -
575A VAL 3.0 10.3 + - - +
576A PHE* 3.3 46.7 - - + -
577A LEU 2.9 25.5 + - - -
614A GLU* 5.1 0.7 - - + -
615A LEU* 1.3 77.2 - - - +
617A LEU* 1.3 70.8 + - - +
618A THR* 4.3 4.0 - - + +
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Residues in contact with LEU 617 (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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321A ILE* 4.0 15.3 - - + -
322A LEU 2.9 7.2 + - - +
323A TYR* 3.1 15.5 - - + -
324A TYR 2.8 22.7 + - - -
577A LEU* 3.6 26.0 - - + -
580A MET* 4.4 14.8 - - + -
608A ILE* 5.6 2.2 - - + -
615A LEU* 3.8 30.5 - - + -
616A VAL* 1.3 75.5 - - - +
618A THR* 1.3 62.0 + - - +
638A LEU* 3.4 27.6 - - + -
641A ILE* 3.5 27.1 - - + -
646A LEU* 4.4 4.3 - - + -
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Residues in contact with THR 618 (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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323A TYR* 4.1 4.9 - - - -
324A TYR* 3.2 27.6 - - + +
332A GLU* 3.2 25.7 + - + +
335A PHE* 4.1 16.2 - - + -
336A VAL* 4.6 12.3 - - + -
576A PHE* 5.2 0.4 - - + -
577A LEU 3.4 4.6 + - - +
578A ILE* 3.3 18.7 - - + +
579A GLY 3.6 0.7 + - - -
580A MET* 2.9 27.9 + - - +
616A VAL* 4.3 9.9 - - + +
617A LEU* 1.3 79.5 - - - +
619A SER* 1.3 60.4 + - - +
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Residues in contact with SER 619 (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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323A TYR* 2.8 28.8 + - - -
324A TYR 3.2 4.7 + - - +
325A GLU* 3.9 13.0 + - - +
326A ALA* 2.9 26.4 + - - +
332A GLU* 3.9 6.5 - - - +
580A MET 3.6 20.2 - - - +
581A GLU* 3.6 14.6 - - - -
618A THR* 1.3 74.5 - - - +
620A ALA* 1.3 62.3 + - - +
634A PRO* 4.6 7.0 - - - +
638A LEU* 4.8 0.7 - - - -
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Residues in contact with ALA 620 (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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326A ALA* 3.5 7.0 - - + -
328A ASN 3.8 18.4 - - - +
329A GLU* 4.0 0.7 - - - +
332A GLU* 4.8 0.7 - - - +
581A GLU* 2.9 22.0 + - - +
619A SER* 1.3 76.1 + - - +
621A GLN* 1.3 64.2 + - - +
622A MET* 3.5 20.0 - - - +
623A ARG* 3.4 26.9 - - + +
632A ASP 4.5 8.0 + - - +
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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