Contacts of the helix formed by residues 521 - 538 (chain A) in PDB entry 3F7F
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 SER 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A LEU* 1.3 76.6 - - - +
522A ASN* 1.3 67.5 + - - +
523A ASP* 3.7 7.1 + - - +
524A VAL* 3.1 29.7 + - - +
525A LEU* 2.9 26.5 + - - +
561A GLN 5.6 0.2 + - - -
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Residues in contact with ASN 522 (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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394A ASP* 3.2 50.6 + - - +
395A LEU* 4.5 2.6 - - - +
396A ASP 3.6 25.5 + - - +
397A ILE* 4.8 7.5 - - + +
520A LEU 5.6 0.2 - - - +
521A SER* 1.3 74.6 - - - +
523A ASP* 1.3 62.7 + - - +
524A VAL 3.2 0.2 + - - -
525A LEU* 3.2 10.3 + - - +
526A ARG* 2.8 44.5 + - + +
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A SER* 3.3 7.2 + - - +
522A ASN* 1.3 80.8 - - - +
524A VAL* 1.3 62.9 + - + +
526A ARG* 3.9 14.6 - - - +
527A SER* 3.2 23.6 + - - -
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Residues in contact with VAL 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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520A LEU* 4.5 10.1 - - + -
521A SER* 3.1 28.4 + - - +
523A ASP* 1.3 77.0 - - + +
525A LEU* 1.3 65.4 + - - +
527A SER* 2.6 23.0 + - - -
528A ILE* 3.1 23.3 + - + +
557A CYS 3.7 20.2 - - - +
558A LEU* 4.0 10.5 - - + -
561A GLN* 3.7 36.8 - - + +
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Residues in contact with LEU 525 (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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397A ILE* 3.5 28.7 - - + -
517A ALA* 4.0 22.2 - - + +
518A SER* 5.9 0.2 - - - -
520A LEU* 4.0 29.2 - - + +
521A SER 2.9 22.4 + - - +
522A ASN* 3.8 8.3 - - - +
524A VAL* 1.3 76.8 - - - +
526A ARG* 1.3 56.3 + - - +
528A ILE* 3.1 11.3 + - + +
529A SER* 2.9 28.6 + - - -
631A LEU* 4.2 20.0 - - + +
632A GLN* 6.3 0.9 - - + -
635A LEU* 4.9 8.7 - - + -
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Residues in contact with ARG 526 (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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396A ASP 3.3 10.7 + - - -
397A ILE* 3.0 58.5 + - + +
398A VAL 3.8 2.2 + - - -
399A THR 2.5 32.7 + - - -
400A LYS* 4.3 1.2 - - - +
401A THR* 3.7 27.8 + - - +
522A ASN* 2.8 39.9 + - - +
523A ASP* 3.9 15.0 - - - +
525A LEU* 1.3 72.3 - - - +
527A SER* 1.3 59.2 + - - +
529A SER* 3.2 2.6 + - - -
530A LYS* 2.9 30.5 + - - +
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Residues in contact with SER 527 (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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523A ASP 3.2 12.1 + - - -
524A VAL* 2.6 23.4 + - - -
526A ARG* 1.3 79.7 - - - +
528A ILE* 1.3 57.1 + - - +
530A LYS* 3.7 7.2 + - - +
531A LYS* 3.2 30.1 + - - +
556A ASN 5.7 0.4 - - - -
557A CYS* 3.4 25.9 + - - +
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Residues in contact with ILE 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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520A LEU* 4.8 3.8 - - + -
524A VAL* 3.1 20.3 + - + +
525A LEU* 3.4 14.6 - - + +
526A ARG 3.1 0.2 - - - -
527A SER* 1.3 77.2 + - - +
529A SER* 1.3 65.0 + - - +
531A LYS* 3.1 6.6 + - - +
532A PHE* 3.0 52.5 + - + -
553A ILE* 4.5 6.7 - - + -
557A CYS* 3.6 21.3 - - + -
558A LEU* 3.3 42.2 - - + -
631A LEU* 4.3 6.7 - - + -
635A LEU* 4.1 13.5 - - + -
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Residues in contact with SER 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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397A ILE* 4.7 2.2 - - - -
525A LEU 2.9 15.2 + - - -
526A ARG* 3.6 8.1 - - - -
528A ILE* 1.3 76.4 - - - +
530A LYS* 1.3 64.0 + - - +
532A PHE 3.0 10.4 + - - -
533A LEU* 3.0 13.2 + - - +
627A TYR* 2.5 29.6 + - - -
631A LEU* 3.8 15.7 - - - -
658A HIS* 2.8 29.2 + - - -
662A PHE* 4.1 9.4 - - - -
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Residues in contact with LYS 530 (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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526A ARG 2.9 16.6 + - - +
527A SER* 3.7 8.7 - - - +
529A SER* 1.3 77.8 - - - +
531A LYS* 1.3 55.9 + - + +
533A LEU* 3.1 23.2 + - + +
534A ASP* 2.9 57.0 + - - +
539A GLU* 3.3 25.6 + - - -
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Residues in contact with LYS 531 (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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527A SER 3.2 15.3 + - - +
528A ILE 3.1 11.0 + - - +
530A LYS* 1.3 76.2 - - + +
532A PHE* 1.3 66.9 + - - +
534A ASP* 3.1 25.6 + - - +
535A ILE* 3.1 11.4 + - - +
540A LEU* 3.5 30.9 - - + +
552A ASP* 3.2 26.3 + - - -
553A ILE* 3.3 27.6 - - + +
556A ASN* 4.0 19.6 - - - +
557A CYS* 3.8 12.3 - - - -
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Residues in contact with PHE 532 (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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528A ILE* 3.0 40.3 + - + -
529A SER* 3.0 6.7 + - - +
531A LYS* 1.3 75.2 - - - +
533A LEU* 1.3 60.6 + - - +
535A ILE* 3.3 21.0 + - + +
536A ILE* 3.5 11.8 + - - +
550A PHE* 4.9 3.8 - + - -
553A ILE* 3.4 28.0 - - + -
631A LEU* 3.6 24.9 - - + -
634A LEU* 3.6 38.1 - - + -
635A LEU* 4.3 1.8 - - - -
638A VAL* 3.8 23.8 - - + -
655A LEU* 3.6 25.0 - - + +
658A HIS* 3.6 16.1 + - + +
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Residues in contact with LEU 533 (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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529A SER 3.0 18.3 + - - +
530A LYS* 3.1 24.0 + - + +
532A PHE* 1.3 73.6 - - - +
534A ASP* 1.3 62.3 + - - +
536A ILE* 3.1 3.7 + - - +
537A THR* 2.8 35.1 + - + +
658A HIS* 3.9 10.5 - - + -
659A TYR* 3.5 45.1 - - + -
662A PHE* 3.5 45.8 - - + -
729A ILE* 3.8 14.8 - - + -
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Residues in contact with ASP 534 (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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530A LYS* 2.9 49.6 + - - +
531A LYS* 3.1 29.2 + - - +
533A LEU* 1.3 74.3 - - - +
535A ILE* 1.3 59.0 + - - +
537A THR* 3.1 6.4 + - - -
538A GLY 2.7 27.9 + - - -
539A GLU* 3.1 39.6 + - + +
540A LEU* 3.3 17.4 + - + -
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Residues in contact with ILE 535 (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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531A LYS 3.1 14.7 + - - +
532A PHE* 3.5 13.2 - - + +
533A LEU 3.2 0.4 - - - -
534A ASP* 1.3 78.9 - - - +
536A ILE* 1.3 65.7 + - + +
538A GLY* 3.6 6.8 + - - -
540A LEU* 3.8 21.8 - - + +
549A LYS* 4.0 41.3 + - + +
550A PHE* 4.2 9.4 - - + -
553A ILE* 4.2 19.5 - - + -
655A LEU* 4.1 31.4 - - + -
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Residues in contact with ILE 536 (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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532A PHE 3.5 9.6 + - - +
533A LEU 3.1 7.4 + - - +
535A ILE* 1.3 83.8 - - + +
537A THR* 1.3 61.2 + - - +
538A GLY* 4.7 0.2 - - - -
652A SER 5.5 1.1 - - - +
655A LEU* 3.6 40.6 - - + +
656A ASP* 4.4 11.2 - - + +
659A TYR* 3.6 37.7 - - + -
714A ILE* 4.1 13.2 - - + -
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Residues in contact with THR 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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533A LEU* 2.8 26.0 + - + +
534A ASP* 3.1 18.4 + - - -
536A ILE* 1.3 74.7 - - - +
538A GLY* 1.3 59.4 + - - +
539A GLU* 3.5 12.3 + - - +
659A TYR* 3.9 20.4 - - + +
725A ARG* 3.5 44.6 + - - +
729A ILE* 5.1 5.6 - - + -
681B LYS* 5.9 0.9 + - - -
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Residues in contact with GLY 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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534A ASP 2.7 14.1 + - - -
535A ILE 3.6 3.6 + - - -
536A ILE 3.3 3.2 - - - -
537A THR* 1.3 75.0 - - - +
539A GLU* 1.3 59.6 + - - -
540A LEU 2.8 14.2 + - - -
541A PRO* 3.2 16.5 - - - +
542A ASP* 5.2 4.5 - - - -
681B LYS* 5.4 6.8 + - - -
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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