Contacts of the helix formed by residues 417 - 432 (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 ARG 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLN* 3.7 26.0 + - + +
198A SER 2.9 29.9 + - - -
199A PHE* 3.7 17.8 - - - +
167B GLU* 3.3 49.2 + - + +
170B SER* 3.0 28.2 + - - -
171B LEU* 3.8 21.7 - - + +
381B ALA* 4.3 2.1 - - - +
414B TYR* 2.8 35.1 + - + +
415B GLY* 2.8 9.7 + - - -
416B ILE* 1.3 81.2 - - - +
418B GLU* 1.3 60.5 + - - +
419B HIS 3.4 2.0 - - - -
420B ALA* 3.5 4.9 + - + -
421B MET* 2.9 28.6 + - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 2.5 29.2 + - - +
1682A THD 2.6 36.6 + - - -
167B GLU* 4.0 0.2 + - - -
381B ALA* 4.3 12.6 - - + +
416B ILE* 4.1 3.5 - - - +
417B ARG* 1.3 75.3 - - - +
419B HIS* 1.3 64.8 + - - +
421B MET* 3.1 10.3 + - - +
422B GLY 2.9 18.5 + - - -
441B THR* 3.8 22.1 + - + +
445B PHE* 3.5 26.2 - - + +
448B TYR* 3.7 10.6 - - + -
449B ALA* 3.4 11.1 - - + +
465B TRP* 3.5 6.9 - - + -
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Residues in contact with HIS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 5.6 0.2 + - - -
448A TYR* 3.8 34.7 + + + -
120B GLN* 3.1 24.0 + - - -
164B ILE* 3.4 30.1 + - + +
167B GLU* 3.5 15.7 + - - +
417B ARG 3.4 0.6 - - - -
418B GLU* 1.3 77.4 + - - +
420B ALA* 1.3 63.0 + - - +
422B GLY* 3.1 10.7 + - - -
423B ALA 3.1 9.7 + - - -
448B TYR* 3.6 19.0 + - + +
449B ALA* 3.4 14.7 - - - +
451B GLY* 3.5 8.0 - - - -
452B ALA* 3.3 22.1 + - + -
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Residues in contact with ALA 420 (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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164B ILE* 3.8 13.2 - - - +
167B GLU* 2.9 40.9 + - + +
168B ALA* 3.6 22.9 - - + +
171B LEU* 5.9 0.4 - - + -
414B TYR* 6.1 0.2 - - + -
417B ARG* 4.0 7.2 - - + +
419B HIS* 1.3 69.1 - - - +
421B MET* 1.3 56.0 + - - +
423B ALA* 3.2 2.3 + - - +
424B ILE* 2.7 45.7 + - + +
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Residues in contact with MET 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER 4.1 0.7 - - - -
381B ALA* 3.9 22.2 - - + -
414B TYR* 3.3 56.7 - - + -
417B ARG 2.9 18.7 + - - +
418B GLU* 3.4 7.6 - - - +
420B ALA* 1.3 76.0 - - - +
422B GLY* 1.3 58.7 + - - +
424B ILE* 3.9 0.5 - - - +
425B MET* 2.9 42.3 + - + +
439B GLY* 3.8 21.1 - - - -
440B GLY 3.5 19.1 - - - +
441B THR* 4.4 2.2 - - - -
465B TRP* 3.5 30.1 - - + -
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU 2.9 11.5 + - - -
419B HIS 3.1 4.6 + - - -
421B MET* 1.3 78.4 - - - +
423B ALA* 1.3 59.4 + - - +
425B MET* 3.5 6.8 + - - +
426B ASN* 3.2 25.5 + - - +
449B ALA* 4.9 0.2 - - - -
452B ALA* 3.7 12.6 - - - -
456B SER* 4.6 1.2 + - - -
463B VAL* 5.2 0.7 - - - +
465B TRP* 3.4 28.0 + - - -
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Residues in contact with ALA 423 (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* 3.6 20.2 - - - +
123B SER* 3.4 28.7 - - - -
124B ASN* 2.9 33.9 + - - +
164B ILE* 3.7 8.7 - - + -
419B HIS 3.1 5.5 + - - -
420B ALA 3.9 1.6 - - - +
422B GLY* 1.3 73.5 - - - +
424B ILE* 1.3 61.3 + - - +
426B ASN* 3.3 3.5 + - - +
427B GLY 3.0 15.2 + - - -
452B ALA* 3.5 5.0 - - - +
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 3.5 20.6 - - - +
126B VAL* 4.0 17.9 - - + -
127B GLY* 3.5 16.7 - - - -
130B MET* 3.6 15.7 - - - -
168B ALA* 4.6 6.7 - - + -
171B LEU* 3.7 29.2 - - + -
414B TYR* 3.8 16.4 - - + -
420B ALA* 2.7 38.0 + - + +
421B MET 3.9 2.7 - - - +
423B ALA* 1.3 69.4 - - - +
425B MET* 1.3 61.6 + - - +
427B GLY* 3.1 2.6 + - - -
428B ILE* 2.9 36.0 + - + +
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Residues in contact with MET 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B TYR* 3.6 16.8 - - + +
421B MET* 2.9 23.4 + - + +
422B GLY* 3.8 3.8 - - - +
424B ILE* 1.3 75.6 - - - +
426B ASN* 1.3 57.2 + - - +
428B ILE* 3.2 2.8 + - - -
429B SER* 2.8 31.7 + - - -
437B PRO* 3.5 18.9 - - + +
438B TYR* 3.4 15.3 - - - +
439B GLY* 3.2 32.8 - - - +
463B VAL* 3.6 17.7 - - + -
464B ILE 3.8 5.8 - - - +
465B TRP* 3.6 48.0 - - + +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 5.1 0.7 - - - -
120B GLN* 5.2 1.2 - - - +
124B ASN* 3.8 10.7 - - - +
422B GLY 3.2 14.6 + - - +
423B ALA* 3.4 13.9 - - - +
424B ILE 3.2 0.4 - - - -
425B MET* 1.3 79.4 - - - +
427B GLY* 1.3 57.5 + - - +
429B SER* 3.4 1.9 + - - -
430B ALA* 2.8 31.1 + - - +
452B ALA* 3.2 18.6 + - - +
455B LEU* 4.4 6.9 - - - +
456B SER* 2.6 36.9 + - - +
461B HIS* 3.6 26.7 + - + +
463B VAL* 3.5 14.5 - - - +
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Residues in contact with GLY 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 3.3 29.8 - - - +
128B MET* 3.4 22.3 - - - +
423B ALA 3.0 12.0 + - - -
424B ILE 3.1 2.6 + - - -
426B ASN* 1.3 75.0 - - - +
428B ILE* 1.3 59.4 + - - +
430B ALA* 3.4 4.6 + - - +
431B PHE* 3.0 24.3 + - - +
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Residues in contact with ILE 428 (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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127B GLY* 3.3 22.0 - - - +
130B MET* 4.5 6.5 - - + -
131B ALA* 4.2 11.0 - - + +
377B ILE* 5.0 7.6 - - + -
412B ILE* 3.9 17.3 - - + -
414B TYR* 3.9 13.9 - - - +
424B ILE* 2.9 34.7 + - + +
425B MET 3.6 4.0 - - - +
427B GLY* 1.3 72.1 - - - +
429B SER* 1.3 67.8 + - - +
431B PHE* 3.3 16.6 + - - +
432B GLY 4.0 0.2 + - - -
435B TYR* 3.5 37.3 - - + +
437B PRO* 3.9 21.5 - - + -
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Residues in contact with SER 429 (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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425B MET 2.8 17.5 + - - -
426B ASN 3.6 4.5 - - - -
428B ILE* 1.3 78.8 - - - +
430B ALA* 1.3 60.6 + - - +
431B PHE 3.2 1.2 + - - -
432B GLY* 3.3 14.0 + - - +
435B TYR 4.2 15.5 + - - +
437B PRO* 4.1 7.8 - - - +
461B HIS* 3.9 7.3 + - - +
462B PRO* 3.5 29.6 - - - +
463B VAL* 3.9 14.9 + - - -
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Residues in contact with ALA 430 (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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60B ARG* 4.5 9.9 + - - -
106B PHE* 4.1 13.4 - - + -
112B GLU* 3.6 25.6 - - - +
113B VAL* 3.7 13.5 - - + -
128B MET* 4.1 5.8 - - + -
426B ASN 2.8 21.7 + - - +
427B GLY 3.7 4.3 - - - +
428B ILE 3.3 0.2 - - - -
429B SER* 1.3 71.6 - - - +
431B PHE* 1.3 66.7 + - - +
432B GLY* 3.2 1.7 + - - -
461B HIS* 3.8 13.2 + - + -
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Residues in contact with PHE 431 (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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58B ILE* 3.6 27.8 - - + +
60B ARG* 4.4 4.0 + - - -
62B ARG* 2.9 66.5 + - - +
128B MET* 3.7 18.6 - - - +
131B ALA* 3.6 12.6 - - + -
132B GLN* 3.9 21.5 - - + -
135B LEU* 3.8 25.6 - - + -
147B SER* 4.9 0.7 - - - -
149B ASN* 3.8 13.9 - - - -
427B GLY 3.0 11.7 + - - +
428B ILE 3.3 12.6 - - - +
429B SER 3.2 0.2 - - - -
430B ALA* 1.3 78.6 - - - +
432B GLY* 1.3 60.7 + - - +
433B ALA* 4.5 0.7 - - + -
435B TYR* 3.9 24.0 - + - -
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.3 1.8 - - - -
429B SER 3.3 9.6 + - - -
430B ALA 3.2 4.7 - - - -
431B PHE* 1.3 81.2 - - - +
433B ALA* 1.3 74.1 + - - +
434B ASN* 3.0 5.1 + - - -
435B TYR* 3.0 22.1 + - - +
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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
------------------------------------------------------------
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