Contacts of the strand formed by residues 614 - 618 (chain A) in PDB entry 2PME
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 PHE 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A ALA* 4.3 5.8 - - + -
561A LYS* 2.8 22.2 + - + +
562A CYS* 3.4 9.6 - - + -
563A SER* 3.1 20.4 + - - -
604A TYR* 5.3 0.2 - - - -
612A VAL* 3.5 10.8 - - - +
613A ALA* 1.3 93.5 - - + +
615A GLY* 1.3 60.8 + - - +
632A LEU* 4.2 12.1 - - + -
633A ARG 3.7 12.6 - - - +
634A ASP* 3.6 22.2 - - - -
652A VAL* 4.2 16.6 - - + -
655A LEU* 3.5 61.0 - - + -
656A ALA* 4.0 8.7 - - - -
662A TRP* 4.7 2.2 - + - -
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Residues in contact with GLY 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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562A CYS* 4.3 0.4 - - - -
563A SER 3.3 11.9 - - - -
604A TYR* 3.3 25.6 - - - -
614A PHE* 1.3 78.5 - - - +
616A VAL* 1.3 63.4 + - - -
631A THR 3.6 0.3 - - - +
632A LEU* 3.2 7.3 - - - +
633A ARG 2.7 35.1 + - - -
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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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562A CYS* 3.9 17.5 - - - -
563A SER 3.0 8.1 + - - -
564A VAL* 3.1 6.9 - - - +
565A LEU 2.8 22.6 + - - -
580A LEU* 3.7 31.0 - - + -
584A LEU* 6.1 0.9 - - + -
604A TYR* 3.4 2.4 + - - -
615A GLY* 1.3 79.5 - - - +
617A THR* 1.3 62.0 + - - +
618A ILE* 3.9 1.9 + - + +
630A ALA* 4.0 11.0 - - + -
631A THR 3.2 7.2 - - - +
632A LEU* 3.8 16.8 - - + -
648A LEU* 3.8 30.7 - - + -
652A VAL* 4.7 6.7 - - + -
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Residues in contact with THR 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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565A LEU* 3.3 14.7 + - - -
567A LEU* 5.1 2.6 - - - +
600A ILE* 3.5 27.0 - - + +
604A TYR* 3.1 27.4 - - + +
616A VAL* 1.3 72.6 - - - +
618A ILE* 1.3 66.3 + - - +
619A ASP* 3.8 7.3 + - - +
622A THR* 4.4 0.3 + - - -
630A ALA* 3.8 4.2 - - - +
631A THR* 3.0 58.6 + - + +
640A GLN* 4.1 6.7 - - - +
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Residues in contact with ILE 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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564A VAL* 5.2 5.4 - - + -
565A LEU 2.6 14.0 + - - +
566A PRO* 3.7 5.0 - - + +
567A LEU* 3.2 25.1 + - - +
573A PHE* 3.5 29.9 - - + -
576A PHE* 4.4 4.0 - - + -
577A VAL* 4.0 31.4 - - + +
580A LEU* 3.9 18.2 - - + -
616A VAL 4.5 3.4 - - - +
617A THR* 1.3 75.6 - - - +
619A ASP* 1.3 60.0 + - - +
622A THR* 3.7 20.0 - - + -
623A VAL* 4.6 2.7 - - + -
630A ALA* 4.4 6.5 - - + -
645A ILE* 3.9 26.7 - - + -
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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