Contacts of the strand formed by residues 536 - 546 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A ARG* 3.4 0.9 - - - -
531A ASP* 2.8 34.3 + - - +
534A SER* 3.2 31.1 - - - +
535A VAL* 1.3 81.4 - - - +
537A VAL* 1.3 63.2 + - - +
538A TYR* 3.7 30.0 - - + +
561A GLN* 3.2 36.1 - - - +
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Residues in contact with VAL 537 (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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131A TYR* 3.7 42.6 - - + -
132A PHE* 3.7 19.9 - - + -
469A LEU* 4.6 2.7 - - + -
528A CYS* 4.4 7.9 - - + -
529A PHE 3.4 9.0 - - - +
530A ARG* 4.2 15.7 - - + +
535A VAL 4.1 2.0 + - - +
536A MET* 1.3 74.3 - - - +
538A TYR* 1.3 69.7 + - - +
539A CYS* 4.5 1.3 - - - -
561A GLN* 3.3 9.6 - - - +
562A VAL* 2.8 51.9 + - + +
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Residues in contact with TYR 538 (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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123A TYR* 5.3 0.2 - + - -
146A LEU* 3.7 27.1 - - + -
206A GLY 3.5 15.1 + - - -
207A PHE* 3.8 13.6 - - + +
208A PRO* 3.9 23.3 - - + -
528A CYS* 3.2 3.8 - - - +
529A PHE* 2.8 57.7 + + + -
531A ASP* 3.9 22.4 - - + -
534A SER* 4.8 0.2 + - - -
536A MET* 3.7 44.4 - - + -
537A VAL* 1.3 73.9 - - - +
539A CYS* 1.3 62.2 + - - +
559A ILE* 4.3 6.7 - - + -
560A ARG 3.5 11.9 - - - +
561A GLN* 4.1 15.1 + - + -
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Residues in contact with CYS 539 (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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469A LEU* 4.6 0.7 - - - -
485A THR* 3.8 6.1 - - - -
526A THR* 4.5 1.8 - - + -
527A THR 3.3 3.6 - - - +
528A CYS* 2.0 46.9 - - - -
529A PHE* 5.3 0.2 - - - -
537A VAL* 4.4 3.1 + - - -
538A TYR* 1.3 75.4 - - - +
540A ILE* 1.3 60.1 + - - +
541A TYR* 3.5 28.3 - - + +
559A ILE* 3.5 5.2 - - - +
560A ARG 2.9 31.8 + - - +
562A VAL* 3.6 27.1 - - + +
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Residues in contact with ILE 540 (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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148A MET* 4.5 2.5 - - + -
151A PHE* 3.7 35.4 - - + -
167A PHE* 4.5 5.4 - - + -
210A PHE* 4.3 28.0 - - + -
525A HIS 3.6 1.6 - - - +
526A THR* 3.3 5.7 - - - +
527A THR* 2.8 54.8 + - + +
529A PHE* 4.4 4.7 - - + -
539A CYS* 1.3 74.3 - - - +
541A TYR* 1.3 61.5 + - - +
542A ILE* 4.0 18.3 - - + +
557A PRO* 3.9 12.8 - - + -
558A PHE 3.1 11.7 - - - +
559A ILE* 4.4 8.7 - - + +
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Residues in contact with TYR 541 (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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142A LEU* 3.4 19.1 - - + +
485A THR* 2.7 21.6 + - - -
486A GLY 3.3 27.4 - - - -
487A SER* 4.2 1.3 - - - -
500A MET* 3.6 35.2 - - + -
501A TYR 4.9 0.2 - - - -
525A HIS 3.6 3.8 - - - -
526A THR* 3.4 30.5 - - + +
539A CYS* 3.5 36.8 - - + +
540A ILE* 1.3 72.1 - - - +
542A ILE* 1.3 61.2 + - - +
543A ILE* 3.3 12.2 + - + -
556A VAL 3.2 3.8 - - - +
558A PHE* 2.7 39.5 + - + +
560A ARG* 3.8 19.3 - - + -
562A VAL* 4.4 0.9 - - - +
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Residues in contact with ILE 542 (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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151A PHE* 4.3 5.6 - - + -
152A ILE* 3.9 11.4 - - + -
165A PRO* 4.0 19.3 - - + +
167A PHE* 3.6 47.1 - - + -
176A TYR* 4.6 1.8 - - + -
523A TYR 3.9 1.2 - - - +
524A GLY* 3.3 3.5 - - - -
525A HIS* 2.7 49.5 + - + +
527A THR* 6.3 0.2 - - - -
540A ILE* 4.0 24.0 - - + +
541A TYR* 1.3 71.4 - - - +
543A ILE* 1.3 57.7 + - - +
555A ILE* 3.5 28.0 - - + -
556A VAL 3.3 3.4 - - - +
557A PRO* 4.2 6.5 - - + -
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Residues in contact with ILE 543 (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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487A SER* 3.8 32.3 - - - +
489A LEU* 5.8 0.9 - - + -
498A PRO* 4.4 20.2 - - + -
500A MET* 3.9 17.0 - - + -
514A PHE* 5.7 0.7 - - + -
521A ALA* 4.4 2.9 - - + -
522A ALA 5.2 1.3 - - - +
523A TYR 3.5 8.3 - - - +
524A GLY* 4.8 0.4 - - - -
541A TYR* 3.6 12.6 - - + +
542A ILE* 1.3 77.6 - - - +
544A GLU* 1.3 77.2 + - - +
545A LEU* 3.5 19.2 + - + +
555A ILE* 3.5 2.9 - - - -
556A VAL* 2.9 30.3 + - - -
558A PHE* 3.6 30.3 - - + -
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Residues in contact with GLU 544 (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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163A ARG* 2.7 39.1 + - - -
164A ILE 2.7 31.4 + - - -
165A PRO* 4.0 10.5 - - + -
521A ALA* 3.1 8.0 - - - +
522A ALA* 2.8 27.0 + - - +
523A TYR* 2.9 50.1 + - - +
543A ILE* 1.3 70.7 - - - +
545A LEU* 1.3 60.3 + - - +
553A PHE* 3.9 15.0 - - + -
554A GLN 3.4 5.4 - - - +
555A ILE* 4.0 15.0 - - + -
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Residues in contact with LEU 545 (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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498A PRO* 4.0 27.6 - - + -
514A PHE* 3.9 29.4 - - + -
519A GLN* 4.1 13.2 - - - +
520A GLU 3.7 2.9 - - - +
521A ALA* 4.3 0.4 - - + -
543A ILE* 3.5 18.1 + - + +
544A GLU* 1.3 76.9 - - - +
546A SER* 1.3 67.9 + - - +
553A PHE* 3.3 8.2 - - - -
554A GLN* 2.9 43.1 + - - +
556A VAL* 3.9 26.2 - - + -
558A PHE* 4.0 12.8 - - + -
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Residues in contact with SER 546 (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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519A GLN* 3.4 15.1 + - - +
520A GLU* 2.9 54.9 + - - -
545A LEU* 1.3 76.6 - - - +
547A SER* 1.3 64.4 + - - +
552A GLN 3.7 10.6 + - - -
553A PHE* 3.9 8.7 - - - -
554A GLN* 4.8 1.9 - - - +
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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