Contacts of the strand formed by residues 521 - 531 (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 ALA 521 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A LEU* 3.8 22.2 - - + -
495A ARG* 3.0 31.7 + - - +
498A PRO* 3.9 24.5 - - + -
519A GLN 3.8 0.4 + - - -
520A GLU* 1.3 79.7 - - - +
522A ALA* 1.3 64.1 + - - +
543A ILE* 4.4 3.1 - - + -
544A GLU 3.1 15.3 - - - +
545A LEU* 4.3 4.5 - - + +
553A PHE* 4.3 6.3 - - - -
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 4.0 12.1 - - - +
462A VAL* 4.1 8.3 - - - +
463A TYR 4.3 1.9 - - - +
489A LEU* 3.8 25.0 - - - +
495A ARG* 4.3 13.2 - - - +
521A ALA* 1.3 78.2 - - - +
523A TYR* 1.3 75.9 + - + +
524A GLY 3.8 0.3 + - - -
543A ILE* 5.2 0.9 - - - +
544A GLU* 2.8 28.5 + - + +
553A PHE* 4.1 11.2 - - + -
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Residues in contact with TYR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 3.9 10.9 + - - -
164A ILE* 3.5 36.2 - - + +
165A PRO* 4.7 2.2 - - + -
291A THR* 4.3 8.1 - - - -
390A GLU* 2.6 38.9 + - - -
405A ARG* 3.2 11.3 + - - -
462A VAL* 3.7 22.2 - - + -
463A TYR* 3.5 27.6 - + + +
495A ARG* 4.7 7.0 - - - -
522A ALA* 1.3 82.5 - - + +
524A GLY* 1.3 58.9 + - - +
525A HIS* 4.6 14.4 - + - +
542A ILE 3.9 0.8 - - - +
543A ILE* 3.5 4.2 - - - +
544A GLU* 2.9 47.9 + - + +
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Residues in contact with GLY 524 (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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463A TYR* 3.3 14.5 + - - -
464A ALA* 3.8 3.5 - - - +
465A ASP* 3.2 28.5 + - - +
487A SER* 3.7 23.9 - - - +
522A ALA 3.8 0.6 + - - -
523A TYR* 1.3 76.1 - - - +
525A HIS* 1.3 63.5 + - - -
526A THR* 4.9 1.1 - - - -
542A ILE 3.3 7.2 - - - -
543A ILE* 4.5 0.9 - - - -
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Residues in contact with HIS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 3.1 45.7 + - + +
166A SER* 4.5 7.4 - - - -
167A PHE* 4.6 8.5 - - + -
291A THR* 3.6 16.7 + - - -
292A GLY* 3.8 7.2 - - - -
293A SER 4.9 0.4 - - - -
392A ARG* 4.1 10.3 - - - +
463A TYR* 3.3 43.8 + + - -
465A ASP* 3.3 9.0 - - - +
523A TYR* 4.6 4.9 - + - +
524A GLY* 1.3 74.6 + - - -
526A THR* 1.3 61.3 + - - +
527A THR* 5.3 0.9 - - - +
540A ILE 3.6 1.7 - - - +
541A TYR* 3.6 0.6 - - - -
542A ILE* 2.7 56.8 + - + +
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Residues in contact with THR 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG* 2.9 18.2 + - - +
394A TYR* 4.6 1.6 + - - -
465A ASP* 2.8 17.7 + - - +
467A TRP* 3.8 19.7 + - + +
485A THR* 3.8 20.2 - - + +
486A GLY* 3.2 23.0 - - - -
487A SER* 3.7 4.5 + - - -
524A GLY 4.9 0.3 - - - -
525A HIS* 1.3 74.1 + - - +
527A THR* 1.3 66.7 + - - +
528A CYS* 4.4 4.5 - - - -
539A CYS* 4.5 0.4 - - + -
540A ILE 3.3 5.6 - - - +
541A TYR* 3.4 36.9 - - + +
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Residues in contact with THR 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 3.7 23.8 - - + -
169A LEU* 4.1 31.6 + - + +
392A ARG* 2.9 26.3 + - - +
467A TRP* 3.8 14.8 - - + -
525A HIS 4.3 0.9 + - - -
526A THR* 1.3 71.7 + - - +
528A CYS* 1.3 70.7 + - - +
529A PHE* 4.3 1.3 - - + -
538A TYR 3.9 0.3 - - - +
539A CYS* 3.3 0.7 - - - -
540A ILE* 2.8 50.4 + - + +
542A ILE* 5.9 0.4 - - - +
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Residues in contact with CYS 528 (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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127A ILE* 5.9 0.2 - - - +
128A ASN 4.9 1.0 + - - -
131A TYR* 3.2 17.4 + - + -
169A LEU* 5.0 1.2 - - - +
467A TRP* 3.2 54.7 - - + +
469A LEU* 4.2 2.0 - - + -
485A THR* 3.6 12.6 - - - -
526A THR* 4.4 1.3 - - - -
527A THR* 1.3 79.2 - - - +
529A PHE* 1.3 67.2 + - - +
537A VAL* 4.4 4.3 - - + -
538A TYR 3.2 4.3 - - - +
539A CYS* 2.0 46.0 - - - -
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Residues in contact with PHE 529 (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* 3.9 28.7 - + + -
126A GLY 3.8 7.0 - - - +
127A ILE* 4.0 15.9 - - + -
131A TYR* 3.1 13.5 - - - +
169A LEU* 3.9 16.2 - - + -
200A ILE* 4.2 9.0 - - + -
208A PRO* 3.6 34.3 - - + -
210A PHE* 3.7 32.1 - + - -
527A THR* 4.3 2.7 - - + -
528A CYS* 1.3 81.3 - - - +
530A ARG* 1.3 63.2 + - - +
531A ASP 4.9 0.2 - - - -
536A MET 4.1 0.2 - - - +
537A VAL* 3.4 3.4 - - - +
538A TYR* 2.8 53.3 + + + +
540A ILE* 4.4 10.8 - - + -
559A ILE* 4.5 1.8 - - + -
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Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG 3.4 7.1 - - - +
123A TYR* 4.0 10.2 - - - -
126A GLY* 2.9 32.3 + - - +
129A GLN* 4.2 9.9 + - - -
130A PHE 5.0 1.6 + - - -
131A TYR* 2.5 67.2 + - + +
132A PHE* 4.9 4.6 - - - -
529A PHE* 1.3 74.6 - - - +
531A ASP* 1.3 72.6 + - - +
532A THR* 3.3 21.6 + - + +
535A VAL* 4.3 23.7 + - - +
536A MET 3.4 11.0 - - - +
537A VAL* 4.2 11.1 - - + +
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Residues in contact with ASP 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 2.6 43.6 + - - +
123A TYR* 4.1 20.6 + - + -
206A GLY 3.6 10.6 - - - +
529A PHE 4.2 0.4 + - - -
530A ARG* 1.3 70.7 - - - +
532A THR* 1.3 52.7 + - - +
533A GLY 2.8 27.5 + - - -
534A SER* 3.1 21.6 + - - +
535A VAL* 2.7 37.1 + - - -
536A MET 2.8 14.6 + - - +
538A TYR* 3.9 14.4 - - + -
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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