Contacts of the strand formed by residues 588 - 596 (chain E) in PDB entry 3EI4
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 PRO 588 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539E ALA* 3.3 22.5 - - + +
540E CYS* 4.2 14.6 - - - -
559E GLY* 4.8 2.2 - - - -
560E LEU 3.9 17.3 - - - +
564E ILE* 3.8 14.6 - - + -
565E SER 4.7 4.5 - - - +
582E LEU* 3.9 17.7 - - + -
586E ILE 3.5 7.1 - - - +
587E ILE* 1.3 94.3 - - + +
589E ARG* 1.3 61.4 + - - +
590E SER 3.9 0.2 - - - -
604E CYS* 4.6 7.0 - - - -
605E ALA 3.7 8.1 - - - +
606E LEU* 3.8 20.9 - - + -
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Residues in contact with ARG 589 (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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539E ALA 5.0 2.2 - - - +
540E CYS* 4.0 11.7 - - - +
587E ILE* 3.6 6.7 + - + +
588E PRO* 1.3 75.6 - - - +
590E SER* 1.3 59.5 + - - +
605E ALA 2.7 14.9 + - - +
606E LEU 4.3 0.9 - - - +
607E GLY* 4.3 8.1 - - - +
635E PRO* 3.7 36.9 - - + +
636E THR 4.8 4.3 - - - +
637E VAL* 3.8 33.3 - - - +
678E TYR* 4.3 18.0 + - - -
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Residues in contact with SER 590 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540E CYS* 3.9 7.3 - - - -
588E PRO 3.9 0.6 - - - -
589E ARG* 1.3 79.8 - - - +
591E ILE* 1.3 63.2 + - - +
604E CYS* 3.5 2.6 - - - -
605E ALA* 2.8 34.6 + - - +
636E THR 3.3 21.3 - - - -
637E VAL* 3.9 7.7 - - - +
638E LEU* 2.9 37.9 + - - +
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Residues in contact with ILE 591 (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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540E CYS* 3.7 19.4 - - - +
541E LEU 3.7 37.8 + - - +
542E ASP* 3.4 9.8 - - - +
557E ALA* 4.0 13.0 - - + +
558E ILE 3.6 32.3 - - - +
559E GLY 4.1 0.7 - - - +
566E ALA* 3.9 22.7 - - + -
567E ARG 5.1 0.2 - - - +
568E ILE* 5.6 0.4 - - + -
590E SER* 1.3 78.6 + - - +
592E LEU* 1.3 67.7 + - - +
602E LEU* 3.8 14.1 - - + -
603E LEU 3.6 13.0 - - - +
604E CYS* 4.3 5.8 - - - -
638E LEU* 4.9 0.4 - - - -
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Residues in contact with LEU 592 (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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542E ASP* 3.8 16.6 - - - +
544E THR* 4.9 4.0 - - + +
590E SER* 5.7 0.2 - - - +
591E ILE* 1.3 77.6 - - - +
593E MET* 1.3 72.1 + - - +
594E THR* 4.6 4.7 - - + -
602E LEU* 3.6 5.1 - - - -
603E LEU* 2.8 55.7 + - + +
638E LEU* 3.7 35.4 - - + +
639E ARG* 4.7 12.3 - - - +
640E THR* 3.7 22.4 - - - +
649E VAL* 4.2 11.0 - - + -
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Residues in contact with MET 593 (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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542E ASP* 3.0 35.5 + - - +
543E ILE* 3.8 4.7 - - - -
544E THR* 3.4 42.2 - - - +
546E LEU* 3.9 18.4 - - + -
553E SER* 4.1 2.5 - - - +
555E LEU* 4.1 26.5 - - - +
557E ALA* 3.7 24.7 - - + +
568E ILE* 4.9 2.2 - - - -
592E LEU* 1.3 82.1 - - - +
594E THR* 1.3 68.0 + - - +
601E TYR 3.3 9.2 - - - +
602E LEU* 3.8 9.2 - - + -
616E LEU* 4.0 19.1 - - + -
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Residues in contact with THR 594 (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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544E THR* 5.4 1.9 - - - +
546E LEU* 3.9 10.4 - - - +
592E LEU* 4.6 8.1 - - + -
593E MET* 1.3 77.9 - - - +
595E THR* 1.3 70.5 + - - +
596E PHE* 3.6 35.4 + - + -
600E HIS* 3.5 1.6 - - - -
601E TYR* 2.7 46.3 + - + +
603E LEU* 4.5 10.5 - - + -
640E THR* 4.9 5.4 + - - +
647E THR* 4.7 6.1 + - - -
649E VAL* 4.3 14.3 - - + +
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Residues in contact with THR 595 (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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546E LEU* 3.6 12.8 - - - +
547E GLY* 3.9 12.1 + - - +
594E THR* 1.3 75.9 + - - +
596E PHE* 1.3 67.3 + - - +
597E GLU 4.1 1.3 + - - -
598E SER* 3.6 22.2 - - - +
599E SER 3.4 7.4 - - - +
600E HIS* 3.3 35.7 + - + +
647E THR* 3.6 20.1 + - - +
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Residues in contact with PHE 596 (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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594E THR* 3.6 19.7 + - + -
595E THR* 1.3 72.1 - - - +
597E GLU* 1.3 72.7 + - - +
598E SER 3.2 0.9 - - - -
599E SER* 2.7 28.5 + - - +
601E TYR* 3.7 30.0 - + + -
603E LEU* 4.4 8.7 - - + -
647E THR 3.3 26.9 - - - -
648E ASN* 4.1 2.5 - - - -
649E VAL* 3.8 25.6 - - + -
659E ILE* 3.9 25.4 - - + -
660E TYR* 4.1 4.5 - - - -
661E SER* 3.9 27.9 + - - -
664E HIS* 5.2 0.2 + - - -
666E LEU* 3.9 24.2 - - + -
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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