Contacts of the strand formed by residues 610 - 615 (chain E) in PDB entry 1AM4
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 610 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577E VAL* 6.1 0.2 - - - -
578E PHE* 4.2 15.5 - + + -
580E VAL* 4.8 10.3 - - + -
598E VAL* 5.5 9.2 - - + -
601E ILE* 3.2 44.6 - - + -
602E THR* 4.1 20.2 - - + -
605E CYS 4.5 4.5 - - - -
606E PRO* 5.0 0.7 - - + -
607E LYS* 4.6 10.5 - - - -
608E THR* 3.0 24.5 - - - -
609E PRO* 1.3 74.1 - - + +
611E LEU* 1.3 60.1 + - - +
612E LEU 4.1 0.2 - - - -
649E LEU 4.4 10.3 - - - -
650E LYS* 3.8 25.0 + - + -
651E ALA* 3.2 12.2 - - + -
652E VAL* 2.4 41.9 + - - +
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Residues in contact with LEU 611 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E VAL* 5.4 1.1 - - + -
578E PHE* 3.0 22.8 + - - +
579E LEU* 3.3 8.6 - - + -
580E VAL* 2.5 35.2 + - - +
610E PHE* 1.3 72.6 - - - +
612E LEU* 1.3 59.6 + - - +
613E VAL* 3.4 2.2 + - + +
652E VAL* 3.5 19.7 - - + -
653E LYS* 2.9 26.9 - - + +
655E VAL* 3.6 31.4 - - + -
668E VAL 4.0 6.3 - - - +
671E GLU* 3.4 28.5 - - + +
672E ALA* 3.5 23.6 - - + -
675E ALA* 4.7 0.9 - - + -
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Residues in contact with LEU 612 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E VAL* 3.4 10.7 - - + +
582E PHE* 3.6 30.5 - - + -
590E PHE* 4.5 2.5 - - + -
593E VAL* 4.1 13.2 - - + -
610E PHE 4.1 1.0 + - - -
611E LEU* 1.3 69.1 - - - +
613E VAL* 1.3 55.2 + - - +
614E GLY 4.0 0.2 - - - -
642E ALA 3.2 26.7 - - - +
645E LEU* 4.0 22.4 - - + -
646E ALA* 4.1 13.0 - - + +
651E ALA* 4.1 14.5 - - + +
653E LYS 3.2 7.2 + - - +
654E TYR* 3.4 34.0 - - + -
655E VAL* 2.7 33.1 + - - +
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Residues in contact with VAL 613 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519E LEU* 4.7 2.0 - - + -
579E LEU* 4.3 24.9 - - + -
580E VAL 2.7 12.9 + - - +
581E CYS* 3.5 13.3 - - - -
582E PHE* 3.1 29.4 + - - +
611E LEU 3.5 13.7 - - - +
612E LEU* 1.3 77.4 - - - +
614E GLY* 1.3 66.3 - - - +
615E THR* 3.5 15.9 + - - +
655E VAL* 3.0 22.4 - - + +
657E CYS* 3.9 15.5 - - - -
668E VAL* 4.4 8.1 - - + -
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Residues in contact with GLY 614 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582E PHE* 3.5 14.4 - - - -
584E VAL* 3.4 24.5 - - - -
613E VAL* 1.3 75.2 - - - +
615E THR* 1.3 62.2 + - - -
617E ILE* 5.1 0.2 - - - -
654E TYR* 3.5 5.8 - - - -
655E VAL 2.8 9.3 + - - +
656E GLU* 3.4 9.6 - - - -
657E CYS 3.0 25.5 + - - -
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Residues in contact with THR 615 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514E VAL 2.8 32.8 - - - +
515E GLY* 4.0 6.7 - - - -
519E LEU* 3.4 32.9 - - + +
581E CYS* 4.4 5.3 - - - +
582E PHE 3.2 10.4 + - - -
583E SER 3.8 0.2 - - - -
584E VAL* 2.9 28.3 + - - +
613E VAL* 3.5 12.3 + - - +
614E GLY* 1.3 77.9 + - - -
616E GLN* 1.3 79.4 - - + +
617E ILE* 3.4 2.7 - - - -
657E CYS* 3.5 7.6 - - - +
659E ALA 5.7 0.4 - - - +
678E GNP 4.5 7.4 - - - +
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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