Contacts of the strand formed by residues 446 - 458 (chain D) in PDB entry 1GPM
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 GLN 446 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401D HIS* 3.3 20.7 - - - +
402D PRO* 2.9 35.3 + - + +
404D PRO* 4.9 1.4 - - - +
411D ARG* 3.4 23.6 - - - +
444D VAL* 3.5 4.6 - - - +
445D SER* 1.3 80.9 - - - +
447D ALA* 1.3 74.9 + - - +
448D PHE* 3.9 18.6 - - + +
473D ARG 4.4 0.2 - - - -
474D ALA* 3.3 3.7 - - - -
475D VAL* 3.2 42.3 + - + +
522D ILE* 4.5 8.5 - - + -
523D GLU* 4.0 3.4 + - - -
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Residues in contact with ALA 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D HIS* 4.0 11.5 + - - +
428D ASP* 4.4 1.2 - - - +
431D PHE* 4.0 6.3 - - + -
432D ILE* 3.4 20.5 - - + +
435D LEU* 3.5 32.5 - - + -
444D VAL* 4.2 7.6 - - + -
446D GLN* 1.3 87.8 + - - +
448D PHE* 1.3 63.0 + - - +
473D ARG 3.2 8.7 - - - +
474D ALA* 4.5 2.0 - - + -
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Residues in contact with PHE 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ARG* 3.1 43.1 - - + +
428D ASP* 3.6 13.9 - - - +
431D PHE* 3.5 7.3 - - - -
446D GLN* 3.9 17.3 - - + -
447D ALA* 1.3 83.1 - - - +
449D THR* 1.3 65.1 + - - +
450D VAL* 4.2 17.0 - - + -
472D LEU 3.6 0.3 - - - -
473D ARG* 2.8 55.9 + - + +
522D ILE* 3.4 35.4 - - + -
523D GLU* 3.2 35.4 - - - -
524D TRP* 5.1 0.4 - + - -
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Residues in contact with THR 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D LEU* 5.7 0.3 - - - +
411D ARG* 4.2 9.0 - - - +
424D LEU* 3.5 36.7 - - + +
427D ALA* 4.0 8.7 + - + +
428D ASP* 3.3 28.9 + - - +
431D PHE* 3.7 13.3 - - - +
448D PHE* 1.3 78.8 - - - +
450D VAL* 1.3 66.8 + - - +
470D VAL* 3.7 27.1 - - + -
471D SER 3.2 12.3 - - - +
472D LEU* 3.7 10.2 - - + +
500D ILE* 5.4 0.2 - - + -
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Residues in contact with VAL 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D ARG* 3.6 13.9 - - + +
413D LEU* 3.7 39.3 - - + -
424D LEU* 4.2 2.9 - - - -
448D PHE* 4.2 17.9 - - + -
449D THR* 1.3 76.6 - - - +
451D PHE* 1.3 63.4 + - - +
452D LEU* 3.9 1.8 - - + -
470D VAL* 3.2 10.4 - - - +
471D SER* 2.8 41.8 + - - +
473D ARG* 4.8 4.0 - - + -
524D TRP* 4.0 36.6 - - + +
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Residues in contact with PHE 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ARG 2.9 16.0 + - - +
412D VAL* 4.0 15.0 - - + -
413D LEU* 3.2 28.7 + - - +
420D TYR* 3.4 58.3 - + + -
423D LEU* 4.0 20.6 - - + -
424D LEU* 4.1 14.8 - - + +
450D VAL* 1.3 71.4 - - - +
452D LEU* 1.3 71.7 + - - +
453D PRO* 3.6 15.7 - - + +
468D TRP* 3.6 39.5 - + + -
470D VAL* 4.2 15.7 - - + -
507D ILE* 4.9 1.6 - - + -
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Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LEU* 4.3 17.5 - - + -
454B VAL* 4.5 7.9 - - + -
413D LEU* 3.4 14.4 - - + -
450D VAL* 4.4 4.3 - - + -
451D PHE* 1.3 78.6 - - - +
453D PRO* 1.3 63.7 - - + +
454D VAL* 2.8 28.6 + - + +
468D TRP* 3.8 6.1 - - - -
469D VAL* 2.9 49.4 + - + +
470D VAL* 4.3 6.1 - - - -
471D SER* 4.3 4.7 - - - +
511D VAL* 4.2 18.2 - - + -
524D TRP* 3.4 34.1 - - + -
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Residues in contact with PRO 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PRO* 5.7 0.2 - - - +
454B VAL* 3.7 24.9 - - + -
413D LEU* 3.7 28.5 - - + +
414D GLY* 5.6 1.1 - - - -
420D TYR* 5.5 6.3 - - + +
451D PHE* 3.6 17.9 - - + +
452D LEU* 1.3 80.7 - - - +
454D VAL* 1.3 59.2 + - - +
468D TRP* 3.3 26.8 - - + -
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Residues in contact with VAL 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LEU* 4.2 20.0 - - + -
452B LEU* 4.5 10.5 - - + -
453B PRO* 3.6 37.2 - - + -
454B VAL* 3.9 17.0 - - + -
452D LEU* 2.8 17.5 + - + -
453D PRO* 1.3 79.0 - - - +
455D ARG* 1.3 64.0 + - - +
468D TRP* 3.5 5.5 - - - -
469D VAL* 3.3 44.2 + - + +
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Residues in contact with ARG 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LEU* 4.4 19.0 - - - +
524B TRP 4.7 1.0 - - - +
525B GLU* 5.4 2.9 - - - +
454D VAL* 1.3 78.2 - - - +
456D SER* 1.3 66.1 + - - +
464D ARG* 5.6 4.6 - - - +
466D TYR* 2.8 51.6 + - + +
467D ASP* 3.1 10.9 - - - +
468D TRP* 3.5 46.8 - - + +
469D VAL* 4.3 0.6 - - - +
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Residues in contact with SER 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B TRP* 3.5 22.2 + - - -
455D ARG* 1.3 77.3 + - - +
457D VAL* 1.3 65.9 + - - +
458D GLY 3.4 0.3 + - - -
465D LYS 4.2 0.4 - - - -
466D TYR* 3.4 11.3 - - - -
467D ASP 3.0 24.9 + - - -
469D VAL* 3.5 15.4 - - - +
508D SER* 3.4 14.3 + - - -
509D ARG* 3.3 30.7 + - - -
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Residues in contact with VAL 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ALA* 4.8 2.9 - - - -
521B THR* 3.5 45.2 + - + +
524B TRP 3.4 15.7 + - - +
525B GLU* 4.2 15.5 - - - +
456D SER* 1.3 75.0 - - - +
458D GLY* 1.3 71.3 + - - +
460D MET* 4.7 7.2 - - - -
465D LYS* 3.2 10.8 - - + +
466D TYR* 4.5 16.6 - - + +
508D SER* 3.8 10.8 - - - +
509D ARG* 4.7 2.3 + - - +
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Residues in contact with GLY 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B PRO 4.3 8.3 - - - +
521B THR* 5.0 0.9 - - - +
456D SER 3.4 1.6 + - - -
457D VAL* 1.3 86.3 - - - +
459D VAL* 1.3 66.7 + - - -
460D MET* 3.4 8.3 + - - +
464D ARG 2.9 15.3 - - - -
465D LYS* 2.7 15.2 + - - -
466D TYR 4.8 0.2 - - - -
467D ASP* 4.9 2.2 - - - -
508D SER* 3.7 18.2 - - - -
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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