Contacts of the strand formed by residues 651 - 660 (chain E) in PDB entry 3E20
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 THR 651 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567E LEU* 4.8 5.6 - - + +
568E GLU* 3.3 15.4 + - - +
644E THR* 4.7 5.4 + - - +
645E LEU 3.7 10.7 + - - +
646E ARG* 4.6 12.1 + - - +
650E THR* 1.3 83.6 + - - +
652E VAL* 1.3 62.8 + - - +
653E ALA 4.2 11.4 - - - +
525J ILE* 3.8 41.0 - - + +
528J ASP* 5.0 4.7 + - - -
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Residues in contact with VAL 652 (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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566E ILE* 3.5 4.0 - - - +
567E LEU* 2.5 34.3 + - - -
568E GLU 3.0 23.6 + - - +
569E LEU* 3.5 21.8 - - + -
570E PRO* 5.0 3.1 - - + -
573E LEU* 6.2 0.2 - - + -
577E TYR* 4.0 19.7 - - + +
645E LEU* 3.1 27.8 + - + +
646E ARG 4.3 0.4 - - - +
647E ASP* 3.7 33.2 - - + +
650E THR* 3.5 6.3 + - + +
651E THR* 1.3 76.7 - - - +
653E ALA* 1.3 60.4 + - + +
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Residues in contact with ALA 653 (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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564E ILE* 3.5 22.4 - - + -
565E ALA 3.2 14.6 - - - +
566E ILE* 3.9 7.9 - - + -
567E LEU* 3.6 2.7 - - - -
569E LEU* 5.5 0.4 - - + -
592E PHE* 5.9 0.4 - - + -
644E THR* 3.4 4.5 - - - -
645E LEU* 2.6 48.8 + - + +
651E THR* 3.8 3.1 - - - +
652E VAL* 1.3 86.1 - - + +
654E VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 654 (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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564E ILE* 3.4 9.5 - - - +
565E ALA* 2.9 43.1 + - + -
567E LEU* 3.4 17.7 - - + -
643E PHE* 3.7 15.7 - - - +
644E THR* 4.1 2.2 - - + +
653E ALA* 1.3 74.6 - - - +
655E GLY* 1.3 63.3 + - - +
525J ILE* 3.5 39.3 - - + -
526J CYS* 5.5 2.0 - - - +
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Residues in contact with GLY 655 (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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563E GLN* 3.2 15.5 - - - -
564E ILE* 4.2 1.3 - - - -
565E ALA 4.6 0.2 - - - -
642E ARG* 3.7 1.9 - - - +
643E PHE* 3.0 45.8 + - - +
654E VAL* 1.3 84.2 - - - +
656E LYS* 1.3 65.8 + - - -
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Residues in contact with LYS 656 (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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562E ALA* 3.1 16.7 - - - +
563E GLN* 3.1 43.4 + - + +
634E PHE* 3.3 58.0 - - + -
641E GLY 3.1 6.3 - - - +
642E ARG* 4.6 4.8 - - + +
643E PHE* 4.1 0.2 - - - -
655E GLY* 1.3 77.7 - - - +
657E VAL* 1.3 63.3 + - - +
658E VAL* 4.5 1.2 - - - +
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Residues in contact with VAL 657 (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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560E PHE* 4.1 15.7 - - + -
561E ILE 3.8 1.1 - - - +
562E ALA* 3.7 8.0 - - + +
583E ILE* 5.0 0.7 - - + -
631E MET* 4.3 12.3 - - + -
632E GLU 3.3 27.6 - - - +
633E ARG* 3.4 8.9 - - - +
634E PHE* 2.9 30.3 + - - +
635E GLU 4.7 0.3 + - - -
640E MET 4.1 4.7 - - - +
641E GLY* 2.9 21.2 + - - +
643E PHE* 4.0 9.5 - - + -
656E LYS* 1.3 72.3 - - - +
658E VAL* 1.3 59.7 + - - +
659E LYS 4.1 10.8 - - - +
660E ILE* 4.1 19.3 - - + -
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Residues in contact with VAL 658 (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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561E ILE* 2.7 48.4 + - + +
562E ALA* 3.8 9.9 - - - +
563E GLN* 4.4 7.0 - - + +
620E ILE* 4.8 9.9 - - + -
633E ARG* 3.4 28.1 + - - +
656E LYS 3.5 3.0 + - - +
657E VAL* 1.3 75.0 - - - +
659E LYS* 1.3 60.8 + - + +
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Residues in contact with LYS 659 (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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560E PHE* 3.3 5.6 - - - +
561E ILE* 2.8 51.9 + - + +
633E ARG* 4.5 6.5 - - - +
657E VAL* 3.8 2.9 - - - -
658E VAL* 1.3 82.2 - - + +
660E ILE* 1.3 75.4 + - - +
661E LEU* 4.4 14.9 - - + +
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Residues in contact with ILE 660 (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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555E HIS* 4.8 20.9 - - + +
556E ALA 4.5 2.5 - - - +
557E THR* 3.7 14.1 - - + -
559E ARG 4.3 2.2 - - - -
560E PHE* 4.4 0.4 - - + -
631E MET* 3.1 51.1 - - + +
632E GLU* 4.5 2.2 - - - +
633E ARG* 4.5 17.4 - - + +
657E VAL* 4.1 10.1 - - + -
659E LYS* 1.3 81.8 - - - +
661E LEU* 1.3 67.4 + - - +
662E ASP* 3.5 26.0 + - - +
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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