Contacts of the helix formed by residues 449 - 460 (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 ALA 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418B GLU* 3.4 13.9 - - + +
419B HIS* 3.4 29.6 - - + +
422B GLY* 4.9 0.4 - - - -
446B VAL 2.8 9.7 + - - +
448B TYR* 1.3 79.7 - - - +
450B ALA* 1.3 63.4 + - - +
451B GLY 3.1 3.1 - - - -
452B ALA 3.0 13.7 + - - -
453B VAL* 3.0 12.1 + - - +
465B TRP* 3.5 24.9 - - + -
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A SER* 3.7 26.0 + - - +
450A ALA* 5.0 1.3 - - + -
446B VAL 3.6 2.9 + - - -
447B SER 3.3 17.1 + - - +
448B TYR 3.5 1.4 - - - -
449B ALA* 1.3 76.6 - - - +
451B GLY* 1.3 63.8 + - - +
453B VAL* 3.9 8.4 - - - +
454B ARG* 3.0 26.7 + - - +
489B HIS* 4.0 26.5 - - + +
490B PHE* 4.8 4.6 - - + -
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A SER* 4.7 4.4 + - - -
448A TYR* 3.7 27.7 - - - +
117B PRO* 5.4 1.7 - - - +
120B GLN* 3.5 9.7 - - - +
419B HIS* 3.5 13.4 + - - -
449B ALA 3.1 1.8 + - - -
450B ALA* 1.3 78.8 - - - +
452B ALA* 1.3 60.2 + - - +
454B ARG* 3.7 6.9 + - - +
455B LEU* 3.7 19.8 + - - +
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Residues in contact with ALA 452 (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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120B GLN* 3.5 21.1 - - - +
419B HIS* 3.3 15.4 + - + +
422B GLY* 3.7 8.5 - - - +
423B ALA* 3.5 29.4 - - - +
426B ASN* 3.2 6.4 + - - +
449B ALA 3.0 7.8 + - - +
451B GLY* 1.3 73.5 - - - +
453B VAL* 1.3 64.2 + - - +
454B ARG 3.1 1.6 - - - -
455B LEU* 3.0 12.3 + - - +
456B SER* 3.0 15.6 + - - -
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL* 4.3 12.6 - - + -
449B ALA 3.0 19.3 + - - +
450B ALA 3.9 3.6 - - - +
452B ALA* 1.3 76.2 - - - +
454B ARG* 1.3 63.4 + - - +
456B SER* 3.0 21.3 + - - -
457B ALA* 3.1 12.1 + - - +
465B TRP* 3.8 36.3 - - + +
490B PHE* 3.5 23.8 - - + -
493B LEU* 4.4 1.6 - - + -
496B ILE* 3.5 29.8 - - + -
523B ILE* 4.6 2.9 - - + -
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASN* 3.2 34.9 + - - +
447A SER* 5.8 3.6 - - - -
479A PRO 2.9 25.1 + - - -
480A THR* 4.1 5.3 + - - +
482A GLN 2.9 25.5 + - - -
484A ILE* 3.8 4.8 - - - +
485A GLU* 2.9 40.0 + - - +
636A PHE* 4.0 22.4 - - + -
450B ALA 3.0 16.8 + - - +
451B GLY* 3.8 8.1 - - - +
452B ALA 3.1 0.2 - - - -
453B VAL* 1.3 78.3 - - - +
455B LEU* 1.3 62.6 + - + +
457B ALA* 3.3 4.3 + - - +
458B LEU* 2.9 29.1 + - + +
493B LEU* 4.0 19.9 - - + +
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Residues in contact with LEU 455 (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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480A THR* 4.3 3.1 - - + -
114B THR* 3.7 42.6 - - + +
117B PRO* 4.0 23.1 - - + -
120B GLN* 3.5 39.0 - - + +
124B ASN* 5.6 1.3 - - - +
426B ASN* 4.4 8.3 - - - +
451B GLY 3.7 8.0 + - - +
452B ALA 3.0 7.5 + - - +
454B ARG* 1.3 79.0 - - + +
456B SER* 1.3 61.5 + - - +
457B ALA 3.1 0.7 - - - -
458B LEU* 4.2 16.2 - - + +
459B SER* 2.8 38.5 + - - +
461B HIS* 4.0 2.0 - - + -
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Residues in contact with SER 456 (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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422B GLY 4.6 1.7 + - - -
426B ASN* 2.6 33.8 + - - +
452B ALA 3.0 8.4 + - - -
453B VAL* 3.0 16.6 + - - -
455B LEU* 1.3 75.3 - - - +
457B ALA* 1.3 59.0 + - - +
460B GLY* 2.9 23.4 + - - -
461B HIS* 2.9 16.0 + - - -
463B VAL* 3.7 11.4 - - - +
465B TRP* 5.1 1.4 + - - -
521B PRO* 3.6 25.5 - - - +
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Residues in contact with ALA 457 (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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636A PHE* 3.7 5.8 - - + -
453B VAL 3.1 5.6 + - - +
454B ARG 3.5 7.6 - - - +
456B SER* 1.3 76.0 - - - +
458B LEU* 1.3 65.6 + - - +
460B GLY 3.5 1.4 + - - -
493B LEU* 3.7 21.1 - - + -
494B PRO 3.2 24.5 - - - +
495B ASN* 2.8 41.8 + - - +
496B ILE* 4.4 0.4 - - + -
521B PRO* 3.7 6.2 - - + +
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Residues in contact with LEU 458 (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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479A PRO* 4.1 18.4 - - + +
480A THR* 3.8 40.6 - - + +
636A PHE* 3.5 42.3 - - + -
105B GLU* 5.8 4.7 - - + -
114B THR* 4.3 7.9 - - + +
454B ARG* 2.9 21.5 + - + +
455B LEU* 4.1 15.0 - - + +
457B ALA* 1.3 79.9 - - - +
459B SER* 1.3 62.5 + - - +
460B GLY* 4.6 0.2 - - - -
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Residues in contact with SER 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.3 29.0 - - - +
107B GLU 5.7 0.2 + - - -
114B THR* 2.6 40.4 + - - +
455B LEU* 2.8 23.6 + - - +
458B LEU* 1.3 73.6 - - - +
460B GLY* 1.3 58.5 + - - +
461B HIS* 3.4 23.6 + - - -
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Residues in contact with GLY 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 4.7 5.2 - - - -
456B SER 2.9 10.3 + - - -
458B LEU 3.3 3.0 - - - -
459B SER* 1.3 81.9 - - - +
461B HIS* 1.3 63.8 + - - +
462B PRO* 3.3 11.3 - - - +
495B ASN* 4.0 6.3 - - - -
518B LYS 3.7 1.7 - - - +
519B HIS* 3.1 39.0 + - - +
521B PRO* 4.8 0.2 - - - -
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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