Contacts of the helix formed by residues 485 - 492 (chain B) in PDB entry 1GPU
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 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ARG* 2.8 48.8 + - - +
489A HIS* 4.1 25.0 + - + +
492A SER* 3.3 38.0 - - - +
493A LEU* 3.5 23.1 - - + +
444B ASN* 4.4 0.7 - - - +
447B SER* 4.6 7.7 + - - +
484B ILE* 1.3 75.9 + - + +
486B THR* 1.3 68.9 + - - +
487B LEU 3.5 1.8 - - - -
488B ALA* 3.3 5.6 + - - +
489B HIS* 2.9 28.6 + - - +
619B ALA* 4.4 1.1 - - - -
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Residues in contact with THR 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 3.5 39.9 - - + +
444B ASN* 4.0 7.6 + - - -
447B SER* 3.7 17.3 + - - +
483B PRO* 3.3 32.1 - - - +
484B ILE 3.5 2.1 + - - -
485B GLU* 1.3 83.7 + - - +
487B LEU* 1.3 62.9 + - - +
489B HIS* 3.3 5.7 + - - +
490B PHE* 3.2 43.5 + - + -
618B LEU* 5.4 0.4 - - - -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 3.9 25.8 - - + -
484B ILE 5.1 0.2 + - - -
485B GLU 3.5 0.6 - - - -
486B THR* 1.3 73.7 - - - +
488B ALA* 1.3 59.8 + - - +
490B PHE* 3.3 3.3 + - + +
491B ARG* 2.8 64.8 + - - +
498B VAL* 3.5 24.4 - - + +
500B ARG* 3.5 31.6 - - + +
523B ILE* 5.5 0.7 - - + -
525B ALA* 4.2 11.0 - - + -
616B GLU* 3.8 7.6 - - - +
618B LEU* 4.1 28.9 - - + +
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Residues in contact with ALA 488 (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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492A SER* 3.5 27.6 - - - +
484B ILE 5.4 0.6 + - - -
485B GLU 3.3 10.4 + - - +
487B LEU* 1.3 77.2 - - - +
489B HIS* 1.3 58.8 + - - +
491B ARG* 3.4 2.4 + - - +
492B SER* 2.8 34.0 + - - +
619B ALA* 4.4 7.6 - - + +
621B THR* 3.5 11.4 - - - +
622B CYS* 3.8 27.4 - - + +
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Residues in contact with HIS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A SER* 5.6 3.2 + - - -
485A GLU* 4.1 21.5 + - + +
489A HIS* 3.4 64.8 + + + +
447B SER* 5.0 7.4 + - - -
450B ALA* 4.0 18.6 - - + +
485B GLU 2.9 12.9 + - - +
486B THR* 3.4 12.2 - - - +
487B LEU 3.2 0.2 - - - -
488B ALA* 1.3 75.7 - - - +
490B PHE* 1.3 93.2 + + - +
492B SER* 3.1 22.6 + - - -
493B LEU* 3.4 6.3 + - + +
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 5.7 1.1 - - + -
446B VAL* 3.9 35.9 - - + -
447B SER* 4.8 5.4 - - - -
450B ALA* 4.8 5.6 - - + -
453B VAL* 3.5 34.5 - - + -
454B ARG 5.7 0.2 - - - -
486B THR* 3.2 40.0 + - + +
487B LEU* 4.2 1.6 - - + +
489B HIS* 1.3 106.0 - + - +
491B ARG* 1.3 64.7 + - - +
492B SER 3.0 2.0 - - - -
493B LEU* 3.1 22.2 + - + +
496B ILE* 3.1 28.6 - - + +
498B VAL* 3.8 19.5 - - + -
523B ILE* 3.5 16.2 - - + -
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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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621A THR* 3.9 10.9 - - + +
487B LEU* 2.8 50.1 + - - +
488B ALA* 3.8 5.2 - - - +
490B PHE* 1.3 77.3 - - - +
492B SER* 1.3 59.5 + - - +
493B LEU 3.3 3.8 - - - +
496B ILE 5.7 1.1 - - - -
498B VAL* 4.1 29.4 + - + +
500B ARG* 4.9 3.6 - - - +
562B THR* 4.1 6.7 + - - +
588B LEU 5.1 1.0 + - - -
589B PRO 5.7 0.6 + - - -
591B PHE* 3.5 62.0 - - + +
616B GLU* 2.9 41.8 + - - -
622B CYS* 3.5 25.7 - - + -
623B TRP* 3.9 0.2 - - - +
625B LYS* 5.3 5.4 + - - +
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLU* 3.4 16.9 + - - +
488A ALA* 3.4 22.2 - - - +
492A SER* 5.5 0.2 + - - -
619A ALA* 3.7 14.3 - - - +
621A THR* 2.4 37.1 + - - +
634A ASP* 5.2 0.9 - - - +
488B ALA* 2.8 17.8 + - - +
489B HIS* 3.3 10.8 - - - -
490B PHE 3.0 0.6 - - - -
491B ARG* 1.3 77.9 - - - +
493B LEU* 1.3 59.4 + - - +
494B PRO* 3.6 7.3 - - - +
622B CYS* 5.3 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
------------------------------------------------------------
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