Contacts of the helix formed by residues 490 - 496 (chain B) in PDB entry 5FWP
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 SER 490 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671A GLU 5.5 2.9 + - - -
488B GLY 3.5 0.4 - - - -
489B GLU* 1.3 81.6 - - - +
491B LYS* 1.3 65.3 + - - +
492B GLU* 3.8 6.9 + - - +
493B GLN* 3.1 27.9 + - - +
494B VAL* 3.1 25.8 + - - +
514B THR* 3.6 9.4 - - - -
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Residues in contact with LYS 491 (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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458B HIS* 2.8 35.2 + - + +
459B THR 5.7 0.4 - - - -
463B GLY 2.7 29.2 + - - -
464B ASP* 2.8 22.5 + - - +
490B SER* 1.3 71.2 - - - +
492B GLU* 1.3 61.8 + - - +
494B VAL* 3.1 6.5 - - - +
495B ALA* 2.8 32.8 + - + +
512B TYR* 4.4 25.4 - - + -
514B THR* 3.3 18.5 - - + +
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A GLU 5.5 7.0 - - - +
672A ASP* 5.3 3.1 - - + +
490B SER* 3.2 6.2 + - - +
491B LYS* 1.3 77.6 - - - +
493B GLN* 1.3 65.9 + - - +
495B ALA* 3.2 7.9 + - - +
496B ASN* 2.8 59.9 + - - +
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Residues in contact with GLN 493 (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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671A GLU 5.7 7.3 + - - +
672A ASP* 5.8 3.6 - - - +
673A PRO* 5.3 20.2 - - + +
488B GLY* 3.7 6.4 - - - -
489B GLU* 2.7 43.7 + - - +
490B SER* 3.1 23.1 + - - +
492B GLU* 1.3 77.5 - - - +
494B VAL* 1.3 62.9 + - + +
496B ASN* 3.3 13.3 + - - +
497B SER* 3.3 12.0 + - - -
601B ASN* 5.0 6.5 + - - -
604B ARG* 5.2 2.8 - - - +
667B GLY* 5.3 10.7 - - - -
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Residues in contact with VAL 494 (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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486B ILE* 3.7 26.9 - - + +
487B THR 3.4 34.8 - - - +
488B GLY* 3.7 8.1 - - - +
490B SER 3.4 13.5 - - - +
491B LYS* 3.1 21.1 - - - +
493B GLN* 1.3 78.3 - - + +
495B ALA* 1.3 65.5 + - - +
497B SER* 3.2 16.9 + - - -
500B VAL* 3.5 11.6 - - - +
512B TYR* 3.4 27.5 - - + -
513B MET 4.9 1.1 - - - +
514B THR* 4.7 2.2 - - + -
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Residues in contact with ALA 495 (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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491B LYS* 2.8 23.5 + - + +
492B GLU* 3.5 13.2 - - - +
494B VAL* 1.3 77.9 - - - +
496B ASN* 1.3 64.6 + - - +
497B SER 3.3 0.8 + - - -
500B VAL* 3.9 1.2 - - - +
504B ARG* 2.9 44.2 + - - +
512B TYR* 4.3 11.0 - - + +
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Residues in contact with ASN 496 (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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672A ASP* 3.5 31.7 + - - +
674A GLN* 3.6 27.1 - - + +
492B GLU* 2.8 47.8 + - - +
493B GLN* 3.7 6.5 - - - +
494B VAL 3.2 0.4 - - - -
495B ALA* 1.3 82.0 - - - +
497B SER* 1.3 61.2 + - - +
498B ALA 3.6 1.2 + - - -
501B GLU* 4.5 6.4 - - - +
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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