Contacts of the strand formed by residues 536 - 546 (chain D) in PDB entry 4JF7
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 MET 536 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530D ARG* 3.5 1.2 - - - -
531D ASP* 2.7 33.8 + - - +
534D SER* 3.1 29.2 + - - +
535D VAL* 1.3 80.0 - - - +
537D VAL* 1.3 60.7 + - - +
538D TYR* 3.5 30.4 + - + -
561D GLN* 3.1 40.8 - - - +
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Residues in contact with VAL 537 (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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131D TYR* 3.7 32.3 - - + -
132D PHE* 3.5 36.0 - - + -
469D LEU* 4.7 2.0 - - + -
528D CYS* 4.3 8.3 - - + -
529D PHE 3.5 9.2 - - - +
530D ARG* 4.1 15.9 - - + +
535D VAL 3.8 1.7 + - - +
536D MET* 1.3 75.8 - - - +
538D TYR* 1.3 69.8 - - - +
539D CYS* 4.4 1.3 - - - -
561D GLN* 3.3 8.9 - - - +
562D VAL* 2.9 45.1 + - + +
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Residues in contact with TYR 538 (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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146D LEU* 3.6 30.1 - - + -
206D GLY 3.6 15.0 + - - -
207D PHE* 3.8 12.0 - - + +
208D PRO* 3.8 24.5 - - + -
528D CYS* 3.3 2.1 - - - +
529D PHE* 2.9 56.1 + + + -
531D ASP* 4.1 22.0 - - + -
534D SER* 4.8 0.9 + - - -
536D MET* 3.5 41.4 - - + -
537D VAL* 1.3 75.7 - - - +
539D CYS* 1.3 62.7 + - - +
559D ILE* 4.4 6.7 - - + -
560D ARG 3.4 12.3 - - - +
561D GLN* 4.0 15.7 - - + -
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Residues in contact with CYS 539 (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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469D LEU* 4.7 0.2 - - - -
485D THR* 3.8 5.8 - - - -
526D THR* 4.6 1.8 - - + -
527D THR 3.3 4.0 - - - +
528D CYS* 2.0 45.1 - - - -
529D PHE* 5.3 0.4 - - - -
537D VAL* 4.4 2.2 - - - -
538D TYR* 1.3 75.3 - - - +
540D ILE* 1.3 60.6 + - - +
541D TYR* 3.4 28.2 - - + +
559D ILE* 3.4 6.6 - - - +
560D ARG 2.9 31.7 + - - +
562D VAL* 3.4 27.6 - - + -
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Residues in contact with ILE 540 (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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148D MET* 4.7 3.4 - - + -
151D PHE* 3.8 20.9 - - + -
167D PHE* 4.5 7.2 - - + -
210D PHE* 4.5 23.1 - - + -
525D HIS 3.6 1.4 - - - +
526D THR* 3.2 5.4 - - - +
527D THR* 2.8 59.6 + - + +
529D PHE* 4.6 4.5 - - + -
539D CYS* 1.3 74.5 - - - +
541D TYR* 1.3 62.3 + - - +
542D ILE* 3.7 23.8 - - + -
557D PRO* 3.6 25.6 - - + -
558D PHE 3.2 12.3 - - - +
559D ILE* 4.4 7.6 - - + +
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Residues in contact with TYR 541 (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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142D LEU* 3.5 18.1 - - + +
485D THR* 2.8 25.2 + - - -
486D GLY 3.5 21.8 - - - -
487D SER* 4.2 2.2 - - - +
500D MET* 3.6 42.2 - - + -
501D TYR 4.9 0.2 - - - -
525D HIS 3.6 4.9 - - - -
526D THR* 3.4 27.4 - - + +
539D CYS* 3.4 39.6 - - + +
540D ILE* 1.3 71.6 - - - +
542D ILE* 1.3 60.8 + - - +
543D ILE* 3.3 10.6 + - + +
556D VAL 3.1 4.0 - - - +
558D PHE* 2.9 38.6 + - - +
560D ARG* 3.8 18.3 - - + +
562D VAL* 4.2 1.2 - - - +
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Residues in contact with ILE 542 (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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151D PHE* 4.4 0.7 - - + -
152D ILE* 4.0 15.3 - - + -
165D PRO* 3.9 19.5 - - + +
167D PHE* 3.5 42.8 - - + -
176D TYR* 4.5 2.5 - - + -
523D TYR 3.8 1.2 - - - +
524D GLY* 3.2 4.3 - - - -
525D HIS* 2.8 47.8 + - + +
527D THR* 6.4 0.2 - - - -
540D ILE* 3.7 28.0 - - + -
541D TYR* 1.3 67.9 - - - +
543D ILE* 1.3 57.6 + - - +
555D ILE* 3.5 27.8 - - + -
556D VAL 3.2 4.3 - - - -
557D PRO* 4.2 7.0 - - + -
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Residues in contact with ILE 543 (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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487D SER* 3.9 32.5 - - - +
489D LEU* 5.8 0.7 - - + -
498D PRO* 4.2 21.3 - - + -
500D MET* 3.8 20.4 - - + -
514D PHE* 5.5 0.7 - - + -
521D ALA* 4.4 3.8 - - + -
522D ALA 5.4 0.9 - - - +
523D TYR 3.6 6.5 - - - +
524D GLY* 4.8 0.7 - - - -
541D TYR* 3.7 9.6 - - + +
542D ILE* 1.3 76.9 - - - +
544D GLU* 1.3 68.7 + - - +
545D LEU* 3.4 25.7 + - + +
554D GLN 3.7 0.3 - - - +
555D ILE* 3.5 2.6 - - - -
556D VAL* 2.8 38.5 + - - +
558D PHE* 3.8 27.6 - - + -
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Residues in contact with GLU 544 (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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162D THR 4.4 0.3 - - - +
163D ARG* 2.7 46.6 + - - +
164D ILE 2.9 25.5 + - - -
165D PRO* 3.9 19.3 - - + -
521D ALA* 3.2 8.3 - - - +
522D ALA* 3.0 23.3 + - + +
523D TYR* 2.9 48.6 + - + +
543D ILE* 1.3 71.5 - - - +
545D LEU* 1.3 59.8 + - - +
553D PHE* 3.9 13.3 - - + -
554D GLN 4.1 2.7 - - - -
555D ILE* 4.3 11.4 - - + +
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Residues in contact with LEU 545 (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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498D PRO* 3.9 28.3 - - + -
514D PHE* 3.4 34.3 - - + -
519D GLN* 4.1 12.8 - - - +
520D GLU 4.0 0.4 - - - -
521D ALA* 4.0 5.6 - - + -
543D ILE* 3.4 21.3 + - + +
544D GLU* 1.3 73.7 - - - +
546D SER* 1.3 66.9 + - - +
547D SER* 6.1 0.2 - - - -
553D PHE* 3.3 6.0 - - - -
554D GLN* 2.8 48.6 + - + +
556D VAL* 4.4 11.0 - - + -
558D PHE* 3.8 15.0 - - + -
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Residues in contact with SER 546 (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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519D GLN* 3.0 19.4 + - - -
520D GLU* 3.0 53.5 + - - +
545D LEU* 1.3 74.3 - - - +
547D SER* 1.3 62.3 + - - +
548D SER 4.4 0.5 + - - -
552D GLN 3.5 10.2 + - - -
553D PHE* 3.8 12.3 - - - -
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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