Contacts of the helix formed by residues 488 - 499 (chain B) in PDB entry 1GGT
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 GLU 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LYS* 4.3 16.2 + - - +
189A GLU 4.1 5.3 + - - -
190A ASP* 4.6 17.3 - - - +
191A ASP 5.0 3.6 - - - +
192A ALA* 4.9 13.5 - - + -
381A THR* 4.2 24.0 - - + +
383A PRO* 4.7 5.9 - - - +
486B GLY 3.7 2.4 + - - -
487B GLN* 1.3 77.6 + - - +
489B GLU* 1.3 65.1 + - - +
491B ARG* 2.8 56.9 + - - +
492B LEU* 3.1 26.2 + - + +
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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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379A TRP* 5.3 6.6 - - - -
381A THR* 3.8 20.2 + - - +
382A ARG 5.3 1.4 + - - -
387A VAL* 4.2 14.9 - - + +
388A GLY 4.8 3.3 + - - -
390A GLY* 4.1 24.6 + - - -
391A GLY 4.8 1.0 + - - -
483B PHE* 3.6 33.2 - - + -
487B GLN* 2.9 28.9 + - - +
488B GLU* 1.3 71.0 - - - +
490B GLU* 1.3 52.2 + - - +
492B LEU* 2.8 17.4 + - - +
493B ALA* 2.7 34.5 + - - +
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Residues in contact with GLU 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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436B ASN* 6.0 1.6 - - - +
483B PHE* 3.8 28.9 - - + +
484B GLN 3.7 13.7 - - - +
485B GLU* 3.8 22.5 - - - +
486B GLY* 2.7 32.7 + - - -
487B GLN* 3.1 9.2 + - - +
488B GLU 3.1 0.2 + - - -
489B GLU* 1.3 77.0 - - - +
491B ARG* 1.3 71.1 + - - +
493B ALA* 4.0 1.3 - - - +
494B LEU* 3.3 26.9 + - - +
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Residues in contact with ARG 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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151A LYS* 5.5 2.4 - - - +
487B GLN 3.6 3.8 + - - +
488B GLU* 2.8 47.8 + - - +
490B GLU* 1.3 86.5 + - - +
492B LEU* 1.3 83.3 + - - +
494B LEU* 3.6 5.0 + - - +
495B GLU* 3.1 56.9 + - - +
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Residues in contact with LEU 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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381A THR* 5.6 2.9 - - - +
382A ARG 5.8 0.7 - - - +
383A PRO* 4.6 22.0 - - + +
385A LEU 6.1 0.7 - - - +
387A VAL* 3.9 16.8 - - + -
488B GLU* 3.1 26.0 + - + +
489B GLU* 2.8 20.0 + - - +
491B ARG* 1.3 96.9 - - - +
493B ALA* 1.3 66.0 + - - +
494B LEU 3.2 1.3 - - - -
495B GLU* 3.2 6.9 + - + +
496B THR* 2.8 30.3 + - - +
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Residues in contact with ALA 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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387A VAL* 4.1 4.4 - - + +
418B LYS 3.6 24.7 - - - +
419B HIS 3.9 17.3 - - - -
420B GLY* 3.9 7.1 - - - +
432B PHE* 4.6 4.7 - - + -
483B PHE* 3.8 14.1 - - + -
489B GLU 2.7 18.2 + - - +
490B GLU* 4.0 4.7 - - - +
492B LEU* 1.3 71.1 - - - +
494B LEU* 1.3 64.9 + - - +
496B THR* 2.8 14.6 + - - -
497B ALA* 3.1 10.9 + - - +
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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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348B LEU* 3.8 25.8 - - + -
432B PHE* 4.3 11.0 - - + -
436B ASN* 4.0 37.0 - - + +
438B ASP* 5.6 6.7 - - - +
490B GLU* 3.3 19.8 + - - +
491B ARG* 3.9 4.0 - - - +
492B LEU 3.2 0.4 - - - -
493B ALA* 1.3 80.7 - - - +
495B GLU* 1.3 67.3 + - - +
496B THR 3.1 0.7 + - - -
497B ALA* 3.4 3.3 + - - +
498B LEU* 3.3 31.1 + - + +
504B LYS* 4.7 10.5 - - + -
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Residues in contact with GLU 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 ARG* 3.1 50.1 + - - +
492B LEU* 3.2 10.4 + - + +
494B LEU* 1.3 78.6 - - - +
496B THR* 1.3 61.7 + - - +
498B LEU* 3.6 27.5 - - + +
499B MET* 3.6 9.9 + - - +
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Residues in contact with THR 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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387A VAL* 3.4 14.0 - - - +
419B HIS 3.9 8.1 - - - +
420B GLY 3.3 20.6 - - - +
421B HIS* 3.9 10.8 - - + +
492B LEU* 2.8 19.3 + - - +
493B ALA 2.8 9.6 + - - -
495B GLU* 1.3 74.2 - - - +
497B ALA* 1.3 57.8 + - - +
498B LEU 3.0 1.8 - - - -
499B MET* 2.7 34.1 + - + +
500B TYR* 3.4 24.9 + - + +
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Residues in contact with ALA 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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348B LEU* 5.3 0.4 - - + -
420B GLY 3.3 16.3 + - - +
422B VAL* 3.5 14.8 - - + +
432B PHE* 3.3 47.3 - - + -
493B ALA 3.1 3.0 + - - +
494B LEU 3.4 4.0 + - - +
496B THR* 1.3 78.3 - - - +
498B LEU* 1.3 61.7 + - - +
500B TYR 3.2 6.2 + - - -
502B ALA* 3.1 26.8 + - + +
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Residues in contact with LEU 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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348B LEU* 3.5 30.1 - - + -
494B LEU* 3.3 22.8 + - + +
495B GLU* 3.6 23.6 - - + +
496B THR 3.0 0.6 - - - -
497B ALA* 1.3 78.1 - - - +
499B MET* 1.3 70.0 + - - +
501B GLY* 3.8 3.6 + - - -
502B ALA 3.3 28.3 - - - +
503B LYS* 4.1 6.3 - - - -
504B LYS* 4.2 27.6 - - + +
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Residues in contact with MET 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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495B GLU 3.6 7.5 + - - +
496B THR* 2.7 17.1 + - + +
498B LEU* 1.3 86.2 - - - +
500B TYR* 1.3 73.4 + - + +
501B GLY 3.4 4.1 + - - -
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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