Contacts of the strand formed by residues 509 - 516 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B ARG* 4.0 19.7 - - - +
498B SER* 4.2 10.6 - - - -
499B ASN 3.6 17.5 - - - +
500B PRO* 4.2 9.2 - - + +
502B SER 3.3 9.0 - - - +
503B LYS* 4.0 19.5 - - + +
504B ASN* 4.7 0.5 + - - -
507B ASN 4.3 2.5 - - - +
508B GLU* 1.4 97.3 - - - +
510B VAL* 1.3 67.9 + - - +
511B GLY* 3.7 1.2 + - - -
614B GLU 4.4 4.0 - - - +
615B GLY* 4.4 2.3 - - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ARG* 3.4 20.9 - - - +
443B ILE* 3.7 18.6 - - + -
444B ASP* 3.5 18.2 - - + +
498B SER* 3.1 3.8 - - - -
499B ASN* 3.1 33.2 + - + -
502B SER* 2.8 26.1 + - - +
503B LYS 4.0 3.1 - - - +
504B ASN* 3.8 17.0 - - - +
508B GLU 3.2 0.6 + - - -
509B PRO* 1.3 75.7 - - - +
511B GLY* 1.3 59.4 + - - +
615B GLY 3.4 12.6 - - - +
616B PHE* 3.7 21.3 - - + +
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Residues in contact with GLY 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ILE* 4.1 3.4 - - - -
496B ILE* 4.6 3.4 - - - -
497B ILE 3.2 13.9 - - - -
498B SER* 3.9 4.5 - - - -
509B PRO 4.6 0.2 - - - -
510B VAL* 1.3 78.6 - - - +
512B TYR* 1.3 60.4 + - - -
614B GLU* 2.9 39.3 + - - -
616B PHE* 3.3 16.1 - - - +
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Residues in contact with TYR 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PHE* 5.2 0.2 - - - -
271B ILE* 3.4 42.5 - - + +
394B GLY* 2.6 36.2 + - - -
396B ILE* 4.1 10.3 - - + -
441B MET* 5.5 0.4 - - + -
443B ILE* 4.0 15.5 - - + -
496B ILE* 3.4 2.5 - - - +
497B ILE* 2.9 33.9 + - + +
511B GLY* 1.3 81.9 - - - -
513B LYS* 1.3 59.7 + - - +
611B LEU* 3.6 33.0 - - + -
612B ARG 3.3 16.8 - - - -
613B PRO* 3.4 22.8 - - + +
614B GLU* 4.0 3.6 - - - +
616B PHE* 3.7 27.6 - + - -
617B PHE* 4.2 5.0 - - - -
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A PHE* 4.7 6.3 + - - +
453B GLU* 2.6 29.7 + - - -
472B ARG* 3.5 14.1 - - - +
494B THR* 3.5 24.6 + - + +
495B TRP 3.5 4.9 - - - +
496B ILE* 3.8 21.8 - - + -
512B TYR* 1.3 73.0 - - - +
514B LEU* 1.3 62.6 + - - +
515B HIS* 3.3 33.6 + - + +
611B LEU* 3.1 5.4 - - - -
612B ARG* 2.7 38.6 + - + +
613B PRO 5.4 0.2 - - - +
614B GLU* 4.0 22.0 + - + +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B LEU* 4.8 3.8 - - + -
494B THR* 3.5 22.2 - - - -
495B TRP* 2.7 36.2 + - + +
497B ILE* 4.6 3.8 - - + -
512B TYR 4.1 0.6 + - - -
513B LYS* 1.3 71.8 - - - +
515B HIS* 1.3 65.1 + - - +
516B ALA 3.9 2.3 + - - +
541B LEU* 3.5 31.6 - - + -
584B VAL* 4.6 8.3 - - + -
586B HIS* 4.1 18.4 - - + +
609B PHE* 3.6 33.0 - - + -
610B LYS 3.5 15.3 - - - +
611B LEU* 3.7 20.8 - - + +
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Residues in contact with HIS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B THR* 3.7 21.5 - - + +
513B LYS* 3.3 38.5 + - + +
514B LEU* 1.3 73.2 - - - +
516B ALA* 1.3 62.6 + - - +
517B HIS* 4.4 3.5 - - - -
609B PHE* 3.5 5.2 - - - +
610B LYS* 2.8 52.1 + - + +
612B ARG* 3.8 42.9 + - + +
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Residues in contact with ALA 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ARG 5.6 3.6 + - - +
494B THR* 5.7 0.2 - - - +
495B TRP* 4.2 18.3 - - + -
514B LEU* 3.9 3.9 + - + -
515B HIS* 1.3 76.2 - - - +
517B HIS* 1.3 63.1 + - - +
518B ASN* 3.1 32.8 + - - +
540B ASP* 5.6 2.5 - - - +
586B HIS* 3.4 34.3 - - + +
609B PHE* 4.6 0.7 - - - -
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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