Contacts of the helix formed by residues 488 - 499 (chain B) in PDB entry 3D7T
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 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360B LEU* 3.5 38.1 - - + -
483B CYS* 3.5 1.6 - - - -
486B GLU 3.5 8.0 - - - +
487B CYS* 1.3 109.3 - - - +
489B GLU* 1.3 64.6 + - - +
490B SER* 3.3 5.4 - - - +
491B LEU* 4.2 3.6 - - + -
492B HIS 3.3 6.9 + - - -
519B TYR* 3.3 25.1 - - + +
524B GLU* 4.8 9.6 - - + +
527B TYR* 5.8 2.2 - - + -
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Residues in contact with GLU 489 (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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483B CYS* 4.3 18.2 - - + -
487B CYS 3.7 0.9 + - - +
488B PRO* 1.3 71.8 - - - +
490B SER* 1.3 60.2 + - - +
492B HIS* 3.7 3.9 + - + +
493B ASP* 3.0 26.9 + - - +
524B GLU* 5.3 1.0 + - - -
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Residues in contact with SER 490 (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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488B PRO* 4.0 0.9 - - - +
489B GLU* 1.3 74.1 - - - +
491B LEU* 1.3 59.7 + - - +
493B ASP* 3.0 14.1 - - - +
494B LEU* 2.9 26.3 + - - +
515B PHE* 4.3 4.4 - - - -
519B TYR* 2.8 21.9 + - - -
523B THR* 3.3 27.4 - - - -
524B GLU* 2.8 27.3 + - - +
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Residues in contact with LEU 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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360B LEU* 5.7 2.5 - - + -
364B VAL* 4.9 11.7 - - + -
452B LEU* 5.0 11.6 - - + +
456B THR* 4.1 14.6 - - + -
487B CYS* 3.6 12.1 - - - -
488B PRO* 3.5 16.8 + - + +
489B GLU 3.3 0.2 - - - -
490B SER* 1.3 76.0 + - - +
492B HIS* 1.3 63.7 + - - +
493B ASP 2.9 4.0 - - - -
494B LEU* 2.8 21.0 + - + +
495B MET* 3.0 49.3 + - + +
515B PHE* 4.7 7.4 - - + -
516B LEU* 4.7 13.2 - - + -
519B TYR* 3.4 32.9 + - + +
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Residues in contact with HIS 492 (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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480B ARG* 5.9 0.2 - - - +
481B MET 2.9 25.9 + - - -
482B PRO* 3.6 5.4 - - + -
483B CYS* 3.3 54.3 + - + +
484B PRO* 4.7 0.4 - - + -
487B CYS* 3.9 3.0 - - - -
488B PRO 3.3 4.9 + - - +
489B GLU* 4.1 5.7 + - - +
491B LEU* 1.3 78.6 - - - +
493B ASP* 1.3 63.1 + - - +
495B MET* 3.3 17.9 - - - +
496B CYS* 3.1 46.7 + - - -
499B TRP* 4.3 7.8 - + - -
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Residues in contact with ASP 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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489B GLU 3.0 16.2 + - - +
490B SER* 3.0 20.2 - - - +
491B LEU 2.9 0.2 - - - -
492B HIS* 1.3 77.4 - - - +
494B LEU* 1.3 65.3 + - - +
496B CYS* 3.0 20.1 + - - +
497B GLN* 3.3 18.5 + - - +
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Residues in contact with LEU 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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448B PHE* 5.3 0.2 - - + -
452B LEU* 4.3 13.9 - - + -
490B SER 2.9 11.2 + - - +
491B LEU* 2.8 12.4 + - + +
493B ASP* 1.3 77.1 + - - +
495B MET* 1.3 62.0 + - - +
497B GLN* 3.0 38.9 - - + +
498B CYS* 3.2 7.5 + - - -
507B PRO* 4.9 0.2 - - + -
511B TYR* 4.2 10.3 - - + -
512B LEU* 3.8 33.4 - - + -
515B PHE* 3.6 50.3 - - + -
516B LEU* 4.0 15.3 - - + -
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Residues in contact with MET 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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449B GLY* 4.4 1.1 - - - +
452B LEU* 4.1 30.1 - - + -
453B THR* 3.8 25.6 - - - +
456B THR* 3.8 17.9 - - - +
484B PRO* 4.5 7.4 - - + -
487B CYS* 3.9 10.5 - - - -
491B LEU* 3.0 39.6 + - + +
492B HIS* 3.3 20.6 - - - +
494B LEU* 1.3 77.1 - - - +
496B CYS* 1.3 56.9 + - - +
498B CYS* 2.9 27.2 + - - +
499B TRP* 3.0 35.5 + - + -
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Residues in contact with CYS 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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480B ARG* 5.3 8.3 - - + +
481B MET 5.1 0.2 - - - -
492B HIS* 3.1 47.3 - - - -
493B ASP* 3.0 10.5 + - - +
495B MET* 1.3 79.2 - - - +
497B GLN* 1.3 60.7 + - - +
499B TRP* 3.1 26.7 + - - -
500B ARG* 3.2 15.2 + - - +
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Residues in contact with GLN 497 (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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276A ASP* 5.8 1.8 + - - -
279A ARG* 5.7 4.2 - - - +
493B ASP* 3.3 14.4 + - - +
494B LEU* 3.0 34.5 - - - +
496B CYS* 1.3 78.9 - - - +
498B CYS* 1.3 57.9 + - - +
500B ARG* 3.3 57.1 + - - +
506B ARG* 3.4 7.8 - - - +
507B PRO* 3.2 28.4 - - + +
511B TYR* 3.6 28.7 + - - -
515B PHE* 5.8 0.5 - - - -
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Residues in contact with CYS 498 (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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445B VAL* 3.7 31.0 - - - +
446B TRP* 3.5 15.8 - - - -
448B PHE* 4.3 8.1 - - - -
449B GLY* 3.8 18.8 - - - -
452B LEU* 5.0 1.1 - - - -
494B LEU* 3.2 14.7 + - - -
495B MET* 2.9 12.5 + - - +
497B GLN* 1.3 80.2 - - - +
499B TRP* 1.3 56.1 + - - +
500B ARG 3.3 0.4 - - - -
506B ARG* 2.9 20.5 - - - +
507B PRO* 3.8 9.2 - - - -
512B LEU* 3.9 24.7 - - - -
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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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446B TRP* 3.4 39.7 + + + -
449B GLY* 3.5 23.5 - - - -
450B ILE* 3.4 27.0 - - + +
453B THR* 3.5 23.8 - - + -
463B TYR* 5.3 1.8 - - - -
480B ARG* 2.8 51.6 + - + +
481B MET* 3.6 43.5 - - + -
482B PRO 5.6 0.2 - - - -
492B HIS* 4.3 6.7 - + - -
495B MET* 3.0 33.5 + - + -
496B CYS* 3.1 19.0 + - - +
498B CYS* 1.3 81.3 - - - +
500B ARG* 1.3 61.9 + - - -
501B LYS 3.2 1.4 + - - -
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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