Contacts of the helix formed by residues 498 - 509 (chain B) in PDB entry 4FE1
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 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B PHE* 3.1 30.1 - - + +
257B LEU* 3.6 14.3 - - + +
495B TYR 5.7 1.8 - - - +
496B GLY* 5.3 1.8 - - - -
497B ASN* 1.3 82.7 - - - +
499B TRP* 1.3 57.8 + - - +
500B LEU 3.1 1.7 - - - +
501B PRO* 3.1 23.0 - - - +
502B GLY 4.7 0.2 + - - -
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Residues in contact with TRP 499 (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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256B PHE* 3.3 69.9 + + + +
257B LEU 3.5 8.2 - - - +
258B GLY* 4.3 6.1 - - - -
496B GLY 3.5 20.6 - - - -
497B ASN* 2.7 45.8 + - - +
498B VAL* 1.3 72.9 - - - +
500B LEU* 1.3 89.3 + - + +
501B PRO 3.4 0.3 - - - -
502B GLY 3.5 1.7 + - - -
503B TRP* 3.0 33.9 + + + +
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Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B LEU* 3.7 30.1 - - + -
489B SER* 3.1 42.8 - - - +
497B ASN* 3.7 21.3 - - + +
498B VAL 3.9 0.2 - - - +
499B TRP* 1.3 93.3 - - + +
501B PRO* 1.4 64.1 - - + +
503B TRP* 3.8 5.8 - - + +
504B LEU* 2.9 62.2 + - + +
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Residues in contact with PRO 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B VAL* 3.1 25.4 - - - +
500B LEU* 1.4 93.9 - - + +
502B GLY* 1.3 57.7 + - - +
504B LEU* 3.2 8.4 + - + +
505B ASP* 2.9 30.5 + - - +
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Residues in contact with GLY 502 (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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257B LEU 3.9 15.1 + - - -
258B GLY 4.1 5.8 - - - -
259B GLY* 3.7 10.1 - - - -
498B VAL 4.7 0.2 + - - -
499B TRP 3.5 2.6 + - - -
501B PRO* 1.3 77.6 - - - +
503B TRP* 1.3 56.6 + - - +
505B ASP* 3.4 7.5 + - - +
506B ALA* 3.0 31.2 + - - +
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Residues in contact with TRP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLY* 5.1 2.5 - - - -
259B GLY* 4.0 16.3 - - - +
358B LEU* 4.2 30.3 - - + -
470B HIS* 2.9 39.6 + + + +
481B LEU* 4.8 4.6 - - + +
499B TRP* 3.0 27.9 + + + +
500B LEU* 3.8 10.5 - - + +
502B GLY* 1.3 76.6 - - - +
504B LEU* 1.3 65.6 + - + +
506B ALA* 3.3 3.2 + - - +
507B ILE* 2.9 35.2 + - + +
514B LEU* 4.1 20.4 - - + +
515B PHE* 4.0 20.9 - + - -
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Residues in contact with LEU 504 (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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470B HIS 3.9 6.5 - - - +
471B GLY* 3.3 38.6 - - - +
481B LEU* 3.4 15.9 - - + +
489B SER* 6.2 0.9 - - - -
500B LEU* 2.9 53.1 + - + +
501B PRO* 3.7 5.6 - - + +
503B TRP* 1.3 76.8 - - + +
505B ASP* 1.3 64.0 + - - +
507B ILE* 3.2 4.4 - - - +
508B ASN* 3.1 34.1 + - - +
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Residues in contact with ASP 505 (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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501B PRO 2.9 16.5 + - - +
502B GLY* 3.5 9.4 - - - +
504B LEU* 1.3 78.3 - - - +
506B ALA* 1.3 63.5 + - - +
508B ASN* 4.0 2.0 - - - +
509B SER* 3.1 31.2 + - - -
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Residues in contact with ALA 506 (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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259B GLY* 3.9 10.8 - - - -
260B PHE* 3.8 25.4 - - + +
502B GLY 3.0 17.4 + - - +
503B TRP* 3.8 1.8 - - - +
505B ASP* 1.3 78.9 - - - +
507B ILE* 1.3 60.8 + - - +
509B SER* 3.3 13.2 + - - -
512B ASN* 3.0 24.9 + - - +
514B LEU* 3.6 17.9 - - + -
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Residues in contact with ILE 507 (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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467B GLN 4.1 8.5 - - - +
470B HIS* 3.8 29.8 - - + +
471B GLY 4.0 11.4 - - - -
472B LYS* 3.8 23.3 + - + +
503B TRP* 2.9 22.0 + - + +
504B LEU* 3.2 20.0 - - - +
506B ALA* 1.3 76.6 - - - +
508B ASN* 1.3 71.0 + - - +
509B SER 5.3 0.2 - - - -
510B GLY* 5.4 0.3 + - - -
512B ASN* 5.5 0.6 - - - +
514B LEU* 3.6 31.6 - - + +
515B PHE* 3.5 33.0 - - + -
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Residues in contact with ASN 508 (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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471B GLY 2.9 23.2 + - - -
472B LYS* 3.5 15.6 + - - +
473B LEU* 3.2 35.3 + - - +
474B LEU* 4.3 2.8 + - - +
504B LEU* 3.1 28.4 + - - +
505B ASP* 4.4 2.2 - - - +
507B ILE* 1.3 81.0 - - - +
509B SER* 1.3 60.6 + - - +
510B GLY* 3.0 8.9 + - - -
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Residues in contact with SER 509 (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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505B ASP* 3.1 21.3 + - - -
506B ALA* 3.3 17.0 + - - -
507B ILE 5.3 0.4 - - - -
508B ASN* 1.3 72.8 - - - +
510B GLY* 1.3 50.9 + - - +
511B THR* 2.3 37.7 + - - -
512B ASN* 3.7 14.7 + - - +
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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