Contacts of the strand formed by residues 436 - 447 (chain D) in PDB entry 4PKY
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 TRP 436 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399D PHE 3.9 2.2 - - - -
401D HIS* 3.3 67.5 + + + -
402D PRO* 4.1 7.4 - - + -
428D ARG* 4.1 16.7 - - + +
429D PHE 3.6 7.6 - - - -
430D ARG* 3.4 62.1 - - + -
435D GLU* 1.3 76.7 - - - +
437D LEU* 1.3 64.1 + - - +
438D TRP* 4.0 4.5 + - - -
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Residues in contact with LEU 437 (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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383D THR 3.5 24.7 - - - +
384D VAL* 4.2 9.0 - - + -
428D ARG* 3.3 2.9 - - - -
429D PHE* 2.7 40.1 + - + +
431D SER* 3.6 28.5 - - - -
435D GLU* 4.4 18.2 - - + +
436D TRP* 1.3 76.6 - - - +
438D TRP* 1.3 63.9 + - - +
439D MET* 3.3 9.7 + - - +
463D ASN* 4.4 22.4 - - - +
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Residues in contact with TRP 438 (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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404D ASP* 4.1 7.9 - - - -
426D MET* 3.7 28.3 - - + -
427D PHE* 3.5 36.1 - - - -
428D ARG* 3.5 38.5 - - + +
436D TRP 4.0 3.3 + - - -
437D LEU* 1.3 70.3 - - - +
439D MET* 1.3 60.5 + - - +
463D ASN* 3.5 8.6 + - - +
464D VAL* 3.1 44.6 + - + -
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Residues in contact with MET 439 (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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363D PHE* 4.0 5.8 - - + -
383D THR* 3.9 12.8 - - + +
384D VAL* 4.2 16.8 - - + -
425D VAL 3.9 0.5 - - - +
426D MET* 3.4 6.8 - - - +
427D PHE* 2.6 58.2 + - + +
429D PHE* 3.5 30.1 - - + -
437D LEU* 4.5 7.4 - - - +
438D TRP* 1.3 81.1 - - - +
440D ARG* 1.3 59.3 + - - +
441D THR* 4.0 2.7 - - - +
461D ASN* 3.5 31.0 - - + -
462D THR 3.6 21.1 - - - +
463D ASN* 3.9 13.2 - - - +
464D VAL* 4.6 2.5 - - - -
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Residues in contact with ARG 440 (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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362D ARG* 4.3 9.3 - - - +
424D SER* 4.4 14.6 - - - +
425D VAL 3.5 9.4 - - - +
426D MET* 4.6 15.3 - - - +
438D TRP 4.3 0.2 - - - -
439D MET* 1.3 72.5 - - - +
441D THR* 1.3 63.0 + - - +
442D SER* 4.2 1.1 - - - +
460D THR 3.3 3.6 - - - +
462D THR* 3.0 59.4 + - - +
464D VAL* 3.1 39.2 - - + +
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Residues in contact with THR 441 (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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396D ILE* 5.8 2.5 - - + -
423D LEU 3.8 0.9 - - - +
424D SER* 3.4 3.3 - - - -
425D VAL* 2.7 57.7 + - + +
427D PHE* 3.1 20.4 - - + -
439D MET* 4.0 0.9 - - - +
440D ARG* 1.3 73.5 - - - +
442D SER* 1.3 59.4 + - - +
443D SER* 3.3 22.9 + - - +
459D CYS* 3.8 13.7 - - + -
460D THR 3.4 3.8 - - - +
461D ASN* 2.7 33.1 + - - +
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Residues in contact with SER 442 (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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422D VAL* 4.1 13.6 - - - +
423D LEU 3.1 11.2 - - - -
424D SER* 4.2 9.6 - - - +
440D ARG* 4.2 1.2 - - - +
441D THR* 1.3 70.8 - - - +
443D SER* 1.3 61.2 + - - +
444D PHE* 4.6 4.6 - - - -
458D ILE 4.2 0.3 - - - +
459D CYS* 3.9 0.9 - - - -
460D THR* 3.2 39.2 + - - -
625F ILE* 4.8 2.4 - - - +
629F GLU* 3.6 27.5 + - - +
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Residues in contact with SER 443 (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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412D PHE* 5.5 2.9 - - - -
415D VAL* 4.1 16.4 - - - +
421D GLN 4.1 0.2 - - - +
422D VAL* 3.3 2.6 - - - +
423D LEU* 2.8 33.6 + - - -
425D VAL* 5.5 1.6 - - - +
441D THR* 3.3 15.7 + - - +
442D SER* 1.3 70.1 - - - +
444D PHE* 1.3 68.9 + - - +
457D ILE* 4.2 5.4 - - - -
458D ILE 3.2 10.3 - - - -
459D CYS* 3.0 25.7 - - - -
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Residues in contact with PHE 444 (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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415D VAL* 4.5 5.6 - - - -
420D GLY 3.7 6.3 - - - +
421D GLN 3.4 19.3 - - - +
422D VAL* 3.9 21.8 - - + -
442D SER* 4.6 5.6 - - - -
443D SER* 1.3 83.1 - - - +
445D THR* 1.3 67.7 + - - +
446D PHE* 4.1 1.1 + - + -
457D ILE* 3.5 4.4 - - - +
458D ILE* 3.0 54.2 + - + -
460D THR* 5.3 0.4 - - - -
624E LEU* 3.6 32.8 - - + -
627E LYS* 3.4 28.3 - - + -
625F ILE* 4.1 28.3 - - + -
628F MET* 5.0 8.1 - - + -
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Residues in contact with THR 445 (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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415D VAL* 3.3 27.0 + - + +
416D VAL* 4.0 8.1 - - + -
419D LYS* 3.2 8.8 - - - -
420D GLY* 2.8 46.9 + - - +
421D GLN 4.5 1.0 + - - -
444D PHE* 1.3 78.5 - - - +
446D PHE* 1.3 60.3 + - - +
447D GLN* 4.0 2.1 + - - +
454D ILE* 3.8 31.3 - - + +
456D TYR 3.5 4.3 - - - -
457D ILE* 3.8 16.8 - - + -
627E LYS* 3.7 10.2 + - - -
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Residues in contact with PHE 446 (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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444D PHE* 4.1 1.9 + - + -
445D THR* 1.3 72.4 - - - +
447D GLN* 1.3 77.2 + - - +
449D PRO* 4.7 9.2 - - + -
454D ILE* 3.6 3.0 - - - -
455D GLU* 2.9 62.7 + - + +
456D TYR* 3.0 29.8 + + + +
458D ILE* 5.1 6.3 - - + +
623E ASP* 3.3 65.5 - - + -
624E LEU* 6.4 0.4 - - + -
626E SER* 4.6 9.6 - - - -
627E LYS* 4.3 22.7 - - + -
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Residues in contact with GLN 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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419D LYS* 3.1 51.7 - - + +
420D GLY* 3.9 3.8 + - - +
445D THR* 4.0 8.7 + - - +
446D PHE* 1.3 95.5 - - - +
448D ASN* 1.3 68.6 + - - +
449D PRO* 3.4 2.9 - - - +
453D GLU* 3.1 16.9 - - - +
454D ILE* 4.5 7.6 - - + -
627E LYS* 6.2 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