Contacts of the strand formed by residues 598 - 613 (chain C) in PDB entry 1ES7
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 VAL 598 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533C VAL* 4.4 15.5 - - + -
590C LEU* 4.9 15.7 - - + -
591C TYR 3.3 6.5 - - - +
592C LEU* 3.4 21.1 - - + -
596C GLU 5.4 0.4 - - - +
597C LYS* 1.3 82.4 - - + +
599C VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C MET 3.6 1.2 - - - +
590C LEU* 3.2 9.0 - - - -
591C TYR* 2.7 62.0 + - + +
593C ASP* 3.7 24.0 - - + +
597C LYS* 3.6 23.3 - - - +
598C VAL* 1.3 78.0 - - - +
600C LEU* 1.3 73.0 + - - +
601C LYS* 5.1 1.1 - - + -
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Residues in contact with LEU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588C SER* 4.3 19.5 - - - +
589C MET* 3.5 18.6 - - - +
590C LEU* 3.5 21.5 - - + +
599C VAL* 1.3 81.9 - - - +
601C LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TYR* 5.6 7.7 - - - -
284B ASP* 4.1 8.5 - - - +
588C SER* 3.4 3.5 - - - -
589C MET 2.9 33.1 + - - +
591C TYR* 3.5 28.5 - - + +
599C VAL* 3.9 1.7 + - + -
600C LEU* 1.3 77.7 - - - +
602C ASN* 1.3 69.0 + - - +
603C TYR* 3.3 50.5 + - + +
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Residues in contact with ASN 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586C ALA* 3.6 9.0 - - - +
587C ILE* 3.5 10.8 + - - +
588C SER* 2.8 25.3 + - - +
601C LYS* 1.3 83.7 + - - +
603C TYR* 1.3 59.3 + - - +
604C GLN* 3.1 35.6 + - - +
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Residues in contact with TYR 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 4.5 10.5 - - - +
282B GLY* 6.0 1.6 - - - -
284B ASP* 3.1 26.0 + - - -
285B PHE* 3.6 31.9 - + - -
531C TRP* 4.3 6.9 - - - -
586C ALA* 3.0 20.6 - - - +
587C ILE* 2.8 22.0 + - + +
589C MET* 3.4 39.5 - - + +
591C TYR* 3.9 14.5 - + - -
601C LYS* 3.3 53.6 - - + +
602C ASN* 1.3 70.7 - - - +
604C GLN* 1.3 61.4 + - - +
606C MET* 3.3 23.5 - - + +
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Residues in contact with GLN 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 2.8 26.2 + - - +
281B GLU* 4.0 16.1 + - - +
586C ALA* 3.6 11.8 + - - +
602C ASN* 3.1 31.3 + - - +
603C TYR* 1.3 72.4 - - - +
605C ASP* 1.3 79.2 + - - +
606C MET 3.2 1.9 + - - -
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Residues in contact with ASP 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 4.1 20.8 - - - +
59A ASN* 4.5 2.0 - - - +
60A HIS* 3.0 28.6 + - - +
281B GLU* 4.8 5.0 - - - +
584C LEU* 3.7 46.9 + - + +
585C SER 3.8 8.7 + - - -
586C ALA* 4.4 0.2 - - - +
604C GLN* 1.3 84.4 + - - +
606C MET* 1.3 59.2 + - - +
607C VAL 3.6 1.6 - - - -
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Residues in contact with MET 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 3.8 21.8 - - - -
60A HIS* 3.3 17.9 - - - -
63A VAL* 4.5 7.2 - - + -
285B PHE* 3.7 28.9 - - + -
523C PHE* 5.5 0.9 - - + -
538C TYR* 3.2 43.8 + - + +
540C ALA* 4.1 0.5 - - - +
585C SER 2.9 6.0 + - - +
587C ILE* 3.9 36.3 - - + -
589C MET* 4.2 8.3 - - + -
603C TYR* 3.3 36.8 - - + +
604C GLN 3.8 2.7 - - - +
605C ASP* 1.3 77.9 - - - +
607C VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C TYR* 4.0 4.9 - - + -
539C HIS 3.6 24.5 - - - +
540C ALA 3.9 2.7 - - - -
541C PHE* 4.2 9.9 - - + -
584C LEU* 3.0 10.5 - - - -
585C SER* 2.9 48.4 + - - +
587C ILE* 3.5 30.1 - - + -
605C ASP 3.6 0.2 - - - -
606C MET* 1.3 80.1 - - - +
608C VAL* 1.3 74.7 + - - +
609C GLU* 3.2 9.8 + - - +
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Residues in contact with VAL 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 3.1 39.2 - - + +
516C ARG* 2.7 45.4 + - + -
540C ALA 3.0 14.4 + - - +
541C PHE* 3.9 10.7 - - + +
542C TYR* 4.3 2.2 - - - +
543C CYS* 3.6 26.0 - - - -
581C PRO* 3.5 19.1 - - + -
583C GLU 3.8 3.8 - - - -
584C LEU* 3.9 2.9 - - + -
607C VAL* 1.3 73.6 - - - +
609C GLU* 1.3 53.8 + - - +
610C GLY 3.7 11.7 - - - +
611C CYS* 3.9 0.2 - - - -
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Residues in contact with GLU 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C ARG* 3.4 27.3 + - - +
583C GLU* 2.7 47.8 + - + +
584C LEU* 4.2 2.9 - - - +
585C SER* 2.6 37.4 + - - -
607C VAL* 3.2 10.7 + - - +
608C VAL* 1.3 75.2 - - - +
610C GLY* 1.3 55.7 + - - +
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Residues in contact with GLY 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C ARG* 4.9 2.9 - - - -
581C PRO* 3.4 7.3 - - - +
582C THR* 2.8 30.4 + - - -
583C GLU* 3.2 13.1 + - - +
608C VAL* 3.6 5.0 - - - +
609C GLU* 1.3 81.3 - - - +
611C CYS* 1.3 64.1 + - - -
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Residues in contact with CYS 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C CYS* 4.3 7.9 - - - -
515C LYS* 4.1 12.6 - - - -
516C ARG* 3.4 35.1 - - + +
543C CYS* 2.0 48.7 - - + -
554C HIS 4.2 6.1 - - - +
555C LEU* 4.8 0.6 - - - +
556C ASN* 3.1 17.5 + - - +
580C VAL 3.5 4.3 - - - -
582C THR* 3.4 7.8 + - - -
608C VAL* 3.9 2.9 - - - -
610C GLY* 1.3 73.9 - - - -
612C GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C CYS* 3.8 11.4 - - - -
555C LEU* 3.1 15.9 - - - -
556C ASN* 3.1 6.7 - - - -
578C CYS 3.3 1.4 - - - +
579C CYS* 3.3 3.3 - - - -
580C VAL* 2.9 33.8 + - - +
582C THR* 3.6 9.1 - - - +
611C CYS* 1.3 77.4 - - - +
613C CYS* 1.3 59.8 + - - -
614C ARG* 3.9 0.4 + - - -
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Residues in contact with CYS 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C CYS* 3.8 17.5 - - - -
547C CYS* 2.0 54.3 - - + -
551C LEU* 4.0 17.3 - - + -
555C LEU* 3.0 21.3 + - + +
556C ASN 4.2 0.6 + - - -
557C SER* 2.9 32.8 - - - -
561C ALA* 3.5 4.3 - - - +
577C ALA* 4.1 4.0 - - + -
578C CYS 3.4 3.4 - - - -
612C GLY* 1.3 70.8 - - - -
614C ARG* 1.3 66.1 + - - +
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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