Contacts of the strand formed by residues 509 - 516 (chain A) in PDB entry 1IVV
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 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ARG* 3.8 28.3 - - - +
498A SER* 4.4 5.3 - - - -
499A ASN 3.6 17.7 - - - +
500A PRO* 4.5 8.7 - - + +
502A SER 3.2 10.1 - - - +
503A LYS* 3.8 18.6 - - + -
507A ASN 4.3 3.6 - - - +
508A GLU* 1.3 90.5 - - + +
510A VAL* 1.3 68.3 + - - +
511A GLY* 3.7 1.0 + - - -
614A GLU 4.6 3.3 - - - +
615A GLY 4.3 0.5 - - - +
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Residues in contact with VAL 510 (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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269A ARG* 3.6 17.3 - - - +
443A ILE* 3.7 19.7 - - + +
444A ASP* 3.5 19.3 - - - +
498A SER* 3.1 2.9 - - - -
499A ASN* 3.1 22.2 + - + -
502A SER* 2.8 28.4 + - - +
503A LYS 4.0 4.5 - - - +
504A ASN* 3.9 16.8 - - + +
508A GLU 3.2 0.2 + - - -
509A PRO* 1.3 76.7 - - - +
511A GLY* 1.3 59.1 + - - +
615A GLY 3.1 19.7 - - - +
616A PHE* 3.6 15.7 - - + +
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Residues in contact with GLY 511 (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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443A ILE* 4.2 4.3 - - - -
496A ILE* 4.5 3.8 - - - -
497A ILE 3.2 12.3 - - - -
498A SER* 4.0 4.7 - - - -
509A PRO 4.6 0.2 - - - -
510A VAL* 1.3 77.5 - - - +
512A TYR* 1.3 73.0 + - - -
614A GLU* 3.0 34.9 + - - -
615A GLY 3.9 1.0 + - - -
616A PHE* 3.3 8.2 - - - +
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Residues in contact with TYR 512 (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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271A ILE* 3.6 43.7 - - + +
394A GLY* 2.7 37.3 + - - -
396A ILE* 4.4 6.1 - - + -
443A ILE* 4.1 15.0 - - + -
496A ILE* 3.4 3.2 - - - +
497A ILE* 3.0 35.9 + - + +
511A GLY* 1.3 86.4 - - - -
513A LYS* 1.3 59.1 + - - +
611A LEU* 3.9 29.8 - - + -
612A ARG 3.2 15.5 - - - -
613A PRO* 3.5 19.6 - - + +
614A GLU* 4.0 3.1 - - - +
616A PHE* 3.6 31.9 - + - -
617A PHE* 4.1 6.2 - - - -
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Residues in contact with LYS 513 (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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453A GLU* 2.7 35.0 + - - -
472A ARG* 3.7 7.7 - - - +
494A THR* 3.2 29.3 + - + +
495A TRP 3.5 5.2 - - - +
496A ILE* 4.0 14.4 - - + +
512A TYR* 1.3 74.4 - - - +
514A LEU* 1.3 63.8 + - - +
515A HIS* 3.4 35.1 + - + +
611A LEU* 3.1 4.9 - - - -
612A ARG* 2.6 39.4 + - + +
614A GLU* 3.7 29.4 + - + +
593B PHE* 4.9 7.9 - - - +
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Residues in contact with LEU 514 (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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439A LEU* 4.3 9.9 - - + -
494A THR* 3.4 22.2 - - - -
495A TRP* 2.8 33.0 + - + +
497A ILE* 4.6 4.5 - - + -
512A TYR 4.0 0.6 + - - -
513A LYS* 1.3 71.8 - - - +
515A HIS* 1.3 76.3 + - - +
516A ALA* 3.8 7.3 + - + +
541A LEU* 3.9 22.7 - - + -
584A VAL* 4.1 14.8 - - + -
586A HIS* 4.1 29.8 - - + +
609A PHE* 4.4 4.7 - - + -
610A LYS 3.5 4.9 - - - +
611A LEU* 4.0 28.0 - - + +
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Residues in contact with HIS 515 (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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494A THR* 3.6 21.2 - - + +
513A LYS* 3.4 39.6 + - + +
514A LEU* 1.3 72.5 - - - +
516A ALA* 1.3 64.0 + - - +
517A HIS* 4.4 3.1 - - - -
609A PHE* 3.5 5.2 - - - -
610A LYS* 2.8 49.1 + - + +
612A ARG* 3.4 41.9 + - + +
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Residues in contact with ALA 516 (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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493A ARG 5.6 3.0 + - - +
495A TRP* 4.1 16.7 - - + -
514A LEU* 3.8 4.5 + - + +
515A HIS* 1.3 76.4 - - - +
517A HIS* 1.3 63.7 + - - +
518A ASN* 3.2 31.5 + - - +
540A ASP* 5.7 1.8 - - - +
586A HIS* 3.5 35.9 - - + -
609A PHE* 4.5 1.8 - - - -
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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