Contacts of the strand formed by residues 509 - 517 (chain D) in PDB entry 5UH6
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 ILE 509 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068C PHE* 3.6 28.3 - - + -
1072C GLU* 3.8 15.0 - - + +
1075C ALA* 4.0 7.4 - - + -
1076C MET* 3.5 35.2 - - + -
1079C TYR* 2.9 31.5 + - + -
497D LEU* 4.3 17.5 - - + -
498D LEU 3.4 7.9 - - - +
499D ASN* 3.3 28.0 - - + +
503D THR* 4.1 5.6 - - + +
506D ARG 3.9 2.0 + - - -
508D GLY* 1.3 77.3 - - - +
510D GLN* 1.3 64.9 + - - +
544D HIS* 5.8 0.4 - - + -
559D MET* 3.8 10.5 - - + -
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Residues in contact with GLN 510 (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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1079C TYR* 4.0 7.6 - - - +
497D LEU* 3.5 5.5 - - - -
498D LEU 2.8 31.8 + - - -
507D LEU* 3.5 45.1 + - - +
509D ILE* 1.3 80.7 - - - +
511D ALA* 1.3 63.4 + - - +
512D PHE* 3.5 22.5 - - + -
528D VAL* 3.9 6.8 - - - +
531D ALA* 3.7 13.5 - - - +
532D PHE* 3.8 12.1 - - + -
559D MET* 3.4 9.6 - - - +
561D SER* 3.3 26.3 - - - +
564D ASN* 4.5 9.7 + - - +
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Residues in contact with ALA 511 (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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495D PRO* 4.8 3.4 - - + -
496D VAL 3.3 9.2 - - - +
497D LEU* 3.9 9.9 - - + -
510D GLN* 1.3 72.5 - - - +
512D PHE* 1.3 68.9 + - - +
555D ALA* 3.2 35.9 - - + +
559D MET* 2.6 22.0 + - + +
560D LEU* 3.6 8.6 - - + +
561D SER* 3.2 22.9 + - - -
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Residues in contact with PHE 512 (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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438D LEU 4.0 4.5 - - - -
439D HIS 3.9 2.7 - - - +
440D GLN 3.4 27.1 - - - -
441D CYS* 3.8 25.4 - - + -
495D PRO* 3.2 11.0 - - - +
496D VAL* 2.9 32.3 + - + +
498D LEU* 3.6 31.6 - - + -
510D GLN* 3.5 33.4 - - + -
511D ALA* 1.3 74.1 - - - +
513D GLU* 1.3 60.7 + - - +
514D PRO* 3.5 0.7 - - - +
524D LEU* 4.7 2.0 - - + -
525D HIS* 5.0 4.0 - - + -
528D VAL* 4.0 24.5 - - + -
532D PHE* 4.3 3.6 - + - -
560D LEU* 4.2 5.2 - - - -
561D SER* 3.2 33.2 - - - -
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Residues in contact with GLU 513 (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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439D HIS* 2.7 44.4 + - - +
440D GLN* 3.2 6.3 - - - +
441D CYS 3.0 21.1 + - - -
493D GLU* 4.0 27.2 + - - +
512D PHE* 1.3 70.3 - - - +
514D PRO* 1.3 71.7 - - + +
515D MET* 3.4 28.5 + - + +
560D LEU* 4.7 1.2 - - - +
34E GLY* 3.9 8.0 - - - -
35E ILE* 3.3 34.9 + - + -
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Residues in contact with PRO 514 (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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441D CYS* 3.9 9.9 - - - +
443D LEU* 3.9 27.8 - - + -
452D PHE* 5.0 1.1 - - + -
491D ILE* 3.2 35.4 - - + +
494D HIS 3.2 29.4 - - - +
495D PRO* 3.9 2.0 - - + -
496D VAL* 4.1 15.3 - - + +
512D PHE 3.5 8.7 - - - +
513D GLU* 1.3 91.0 - - + +
515D MET* 1.3 68.2 + - - +
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Residues in contact with MET 515 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D LEU* 5.4 6.5 - - + -
440D GLN* 3.5 40.8 - - + +
441D CYS 3.0 17.7 + - - +
442D GLY* 3.7 4.6 - - - -
443D LEU* 2.9 23.4 + - - +
491D ILE* 4.4 1.8 - - - -
513D GLU* 3.4 34.1 - - + +
514D PRO* 1.3 84.3 - - - +
516D LEU* 1.3 70.3 + - - +
517D VAL* 3.8 0.7 - - - +
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Residues in contact with LEU 516 (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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182B ARG* 5.4 8.3 - - - -
187B THR* 5.6 2.1 - - - +
443D LEU* 3.4 11.4 - - + +
445D LYS* 4.3 24.6 - - + -
448D ALA* 3.6 30.5 - - + -
484D TRP* 5.0 5.6 - - + +
487D LEU* 3.9 27.4 - - + -
488D GLU* 3.2 44.3 + - + +
491D ILE* 4.0 21.6 - - + +
515D MET* 1.3 77.2 - - - +
517D VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 517 (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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187B THR* 5.5 3.6 - - - +
442D GLY* 3.6 20.0 - - - +
443D LEU 3.2 26.4 + - - +
444D PRO* 3.5 6.3 - - + +
445D LYS* 3.1 30.7 + - - +
515D MET 3.8 1.3 - - - +
516D LEU* 1.3 77.0 - - - +
518D GLU* 1.3 77.8 + - - +
519D GLY 3.7 0.5 + - - -
521D ALA 4.6 6.7 - - - +
523D GLN* 3.7 31.2 - - - +
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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