Contacts of the helix formed by residues 417 - 432 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.3 50.1 + - + +
170A SER* 3.0 28.1 + - - -
171A LEU* 3.8 23.8 - - + +
381A ALA* 4.3 2.8 - - - +
414A TYR* 2.7 43.4 + - + +
415A GLY* 2.9 15.0 + - - -
416A ILE* 1.3 81.1 - - - +
418A GLU* 1.3 65.2 + - - +
419A HIS 3.4 2.5 - - - -
420A ALA* 4.2 4.3 - - + -
421A MET* 2.9 22.6 + - - +
161B GLN* 3.7 21.5 + - + +
162B GLU* 4.7 0.2 - - - -
198B SER 2.8 30.1 + - - -
199B PHE* 3.7 15.6 - - - +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 4.3 12.4 - - + +
416A ILE* 4.2 3.5 - - - +
417A ARG* 1.3 73.0 - - - +
419A HIS* 1.3 63.9 - - - +
421A MET* 3.1 8.9 + - - +
422A GLY 2.9 19.1 + - - -
441A THR* 3.7 22.6 + - + +
445A PHE* 3.6 26.4 - - - +
448A TYR* 3.7 11.4 - - + -
449A ALA* 3.5 11.4 - - + +
465A TRP* 3.6 8.6 - - + -
162B GLU* 2.5 29.5 + - - +
1682B THD 2.6 37.2 + - - -
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Residues in contact with HIS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 3.0 25.3 + - - -
164A ILE* 3.3 29.3 + - + +
167A GLU* 3.6 14.8 + - - +
417A ARG 3.4 0.4 - - - -
418A GLU* 1.3 77.4 + - - +
420A ALA* 1.3 64.3 + - - +
422A GLY* 3.1 10.0 + - - -
423A ALA 3.1 9.7 + - - -
448A TYR* 3.5 20.3 + - + +
449A ALA* 3.4 13.2 - - - +
451A GLY* 3.6 7.2 - - - -
452A ALA* 3.3 22.8 + - + -
162B GLU* 5.6 0.2 + - - -
448B TYR* 3.8 34.1 + + + -
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ILE* 3.8 13.8 - - - +
167A GLU* 2.8 41.6 + - + +
168A ALA* 3.6 22.2 - - + +
171A LEU* 5.8 0.4 - - + -
414A TYR* 6.2 0.2 - - + -
417A ARG* 4.1 6.7 - - + +
418A GLU 3.3 0.2 - - - -
419A HIS* 1.3 72.7 - - - +
421A MET* 1.3 52.2 + - - +
423A ALA* 3.2 1.9 + - - +
424A ILE* 2.7 46.2 + - + +
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Residues in contact with MET 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER 4.1 0.4 - - - -
381A ALA* 3.9 22.7 - - + -
414A TYR* 3.3 56.8 - - + -
417A ARG 2.9 19.5 + - - +
418A GLU* 3.1 7.2 + - - +
420A ALA* 1.3 75.7 - - - +
422A GLY* 1.3 57.0 + - - +
424A ILE* 3.8 0.5 - - - +
425A MET* 2.9 42.7 + - + +
439A GLY* 3.8 21.1 - - - -
440A GLY 3.5 19.5 - - - +
441A THR* 4.4 1.8 - - - -
465A TRP* 3.5 30.1 - - + -
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Residues in contact with GLY 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU 2.9 11.7 + - - -
419A HIS 3.1 4.0 + - - -
421A MET* 1.3 78.2 - - - +
423A ALA* 1.3 60.5 + - - +
425A MET* 3.4 6.1 + - - +
426A ASN* 3.2 26.0 + - - +
452A ALA* 3.7 12.6 - - - -
456A SER* 4.6 1.4 + - - -
463A VAL* 5.4 0.5 - - - +
465A TRP* 3.4 28.7 - - - -
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Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 3.6 23.6 - - - +
123A SER* 3.4 29.6 - - - -
124A ASN* 2.8 30.1 + - - +
164A ILE* 3.6 9.6 - - + -
419A HIS 3.1 5.7 + - - -
420A ALA 3.9 1.3 - - - +
422A GLY* 1.3 72.2 - - - +
424A ILE* 1.3 61.2 + - - +
426A ASN* 3.3 3.7 + - - +
427A GLY 3.0 14.4 + - - -
452A ALA* 3.5 5.8 - - - +
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 3.6 20.9 - - - +
126A VAL* 4.0 19.1 - - + -
127A GLY* 3.6 7.6 - - - -
130A MET* 3.7 20.4 - - - -
168A ALA* 4.7 6.1 - - + -
171A LEU* 3.6 30.7 - - + -
414A TYR* 3.7 24.5 - - + +
420A ALA* 2.7 41.6 + - + +
421A MET 3.8 3.4 - - - +
423A ALA* 1.3 69.2 - - - +
425A MET* 1.3 61.3 + - - +
427A GLY* 3.0 2.3 + - - -
428A ILE* 2.9 31.6 + - + +
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Residues in contact with MET 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A TYR* 3.6 16.6 - - - +
421A MET* 2.9 23.8 + - + +
422A GLY* 3.7 3.6 - - - +
424A ILE* 1.3 76.7 - - - +
426A ASN* 1.3 63.0 + - - +
428A ILE* 3.2 2.6 + - - -
429A SER* 2.9 25.6 + - - -
437A PRO* 3.4 18.0 - - + +
438A TYR* 3.3 16.6 - - - +
439A GLY* 3.2 31.6 - - - +
463A VAL* 3.7 16.4 - - + -
464A ILE 3.7 11.4 - - - +
465A TRP* 3.6 43.7 - - + +
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Residues in contact with ASN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 5.2 0.7 - - + -
120A GLN* 5.3 1.0 - - - +
124A ASN* 3.8 11.7 - - - +
422A GLY 3.2 13.5 + - - +
423A ALA* 3.4 13.9 - - - +
424A ILE 3.2 0.6 - - - -
425A MET* 1.3 77.6 - - - +
427A GLY* 1.3 56.3 + - - +
429A SER* 3.4 1.7 + - - -
430A ALA* 2.8 31.3 + - - +
452A ALA* 3.3 17.8 + - - +
455A LEU* 4.4 6.5 - - - +
456A SER* 2.6 36.5 + - - +
461A HIS* 3.6 26.3 + - + +
463A VAL* 3.4 16.0 - - - +
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Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 5.0 0.4 - - - -
124A ASN* 3.3 30.7 - - - +
128A MET* 3.4 22.2 - - - +
423A ALA 3.0 11.4 + - - -
424A ILE 3.0 2.2 + - - -
426A ASN* 1.3 76.2 - - - +
428A ILE* 1.3 63.4 + - - +
430A ALA* 3.4 4.2 + - - +
431A PHE* 3.0 19.8 + - - +
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY* 3.4 21.8 - - - +
130A MET* 4.8 7.2 - - + -
131A ALA* 4.2 11.7 - - + +
377A ILE* 4.9 8.3 - - + -
412A ILE* 3.9 28.0 - - + -
414A TYR* 4.0 9.6 - - - +
424A ILE* 2.9 23.7 + - + +
425A MET 3.7 6.1 - - - +
427A GLY* 1.3 75.0 - - - +
429A SER* 1.3 64.3 + - - +
431A PHE* 3.3 17.2 + - - +
432A GLY 3.9 0.2 + - - -
435A TYR* 3.5 36.6 - - + +
437A PRO* 4.0 21.5 - - + -
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A MET 2.9 17.1 + - - -
426A ASN 3.6 4.0 - - - -
428A ILE* 1.3 79.2 - - - +
430A ALA* 1.3 62.1 + - - +
431A PHE 3.3 0.9 + - - -
432A GLY* 3.3 14.0 + - - +
435A TYR 4.3 10.9 + - - +
437A PRO* 4.1 13.9 - - - +
461A HIS* 4.0 7.4 + - - +
462A PRO* 3.6 27.6 - - - +
463A VAL* 4.0 15.0 - - - -
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 4.5 9.7 + - - -
106A PHE* 4.1 12.4 - - + -
112A GLU* 3.6 25.6 - - - +
113A VAL* 3.8 13.2 - - + -
128A MET* 4.1 7.2 - - + -
426A ASN 2.8 17.9 + - - +
427A GLY 3.7 4.7 - - - +
429A SER* 1.3 72.9 - - - +
431A PHE* 1.3 67.3 + - - +
432A GLY* 3.2 1.8 + - - -
461A HIS* 3.9 13.2 + - + -
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 3.7 18.1 - - + +
60A ARG* 4.3 4.2 + - - -
62A ARG* 3.0 64.6 + - - +
128A MET* 3.6 19.5 - - - -
131A ALA* 3.5 12.6 - - + -
132A GLN* 3.8 25.4 - - + -
135A LEU* 3.7 30.1 - - + -
147A SER* 4.9 0.2 - - - -
149A ASN* 3.8 15.3 - - - -
427A GLY 3.0 11.3 + - - +
428A ILE 3.3 12.8 - - - +
429A SER 3.2 0.2 - - - -
430A ALA* 1.3 78.7 - - - +
432A GLY* 1.3 61.6 + - - +
433A ALA* 4.5 0.7 - - + -
435A TYR* 3.8 24.2 - + - -
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Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 4.4 1.3 - - - -
428A ILE 3.9 0.2 + - - -
429A SER 3.3 10.4 + - - -
430A ALA 3.2 3.7 - - - -
431A PHE* 1.3 81.4 - - - +
433A ALA* 1.3 73.8 + - - +
434A ASN* 3.0 5.9 + - - -
435A TYR* 3.0 21.5 + - - +
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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