Contacts of the helix formed by residues 514 - 527 (chain A) in PDB entry 5FN2
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 ASP 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A GLU* 3.7 24.0 - - - +
314A LYS* 3.9 27.3 + - - +
512A GLN* 3.2 12.7 + - + +
513A ALA* 1.3 74.1 - - - +
515A PRO* 1.4 73.0 - - + +
516A GLN* 3.2 7.5 + - + +
517A THR* 2.7 35.4 + - - +
518A VAL* 3.7 5.5 + - - +
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Residues in contact with PRO 515 (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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480A VAL* 4.0 11.0 - - + +
484A ALA* 4.7 2.4 - - - +
485A LYS* 4.4 26.5 - - + +
488A ALA* 3.5 28.7 - - + -
512A GLN* 6.2 0.9 - - - +
513A ALA 3.1 4.9 - - - +
514A ASP* 1.4 81.3 - - + +
516A GLN* 1.3 63.3 + - + +
517A THR 3.2 0.2 - - - -
518A VAL* 3.2 5.1 + - + +
519A THR* 2.9 28.9 + - - -
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Residues in contact with GLN 516 (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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478A ASN* 3.2 48.8 + - - +
480A VAL* 4.0 7.0 - - + +
514A ASP* 3.2 6.9 + - + +
515A PRO* 1.3 80.3 - - + +
517A THR* 1.3 58.4 + - - +
519A THR* 3.0 13.1 - - - +
520A ARG* 2.9 53.1 + - - +
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Residues in contact with THR 517 (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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307A ALA* 5.4 2.2 - - - -
310A GLU* 4.2 19.7 + - + +
514A ASP* 2.7 33.9 + - - -
516A GLN* 1.3 78.8 + - - +
518A VAL* 1.3 61.2 - - + +
520A ARG* 3.2 20.7 + - - +
521A LEU* 2.9 42.9 + - + +
533A TRP* 5.3 4.4 - - + -
574A LEU* 4.3 21.5 - - + -
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Residues in contact with VAL 518 (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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303A VAL* 3.8 18.2 - - + +
304A THR 5.6 0.2 - - - +
307A ALA* 3.2 32.5 - - + -
484A ALA 4.0 8.1 - - - +
487A LEU* 3.9 28.0 - - + -
488A ALA* 4.0 17.7 - - + -
513A ALA* 4.5 1.3 - - + -
514A ASP 3.9 13.0 - - - +
515A PRO 3.2 7.1 + - - +
517A THR* 1.3 77.4 - - - +
519A THR* 1.3 58.2 + - - +
521A LEU* 3.2 11.2 + - - +
522A LEU* 2.9 32.5 + - + +
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Residues in contact with THR 519 (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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467A TYR* 3.2 22.4 + - - -
476A ASP 4.1 1.3 - - - +
477A LEU 3.2 16.8 - - - +
478A ASN 4.1 2.7 - - - +
479A PHE 3.7 15.9 + - - +
480A VAL* 3.8 22.3 - - + -
481A THR* 4.2 0.5 - - - +
484A ALA* 3.6 25.0 - - - +
515A PRO 2.9 11.5 + - - -
516A GLN* 3.0 21.1 + - - +
518A VAL* 1.3 75.7 - - - +
520A ARG* 1.3 56.6 + - - +
522A LEU* 3.2 6.1 + - - +
523A TYR* 2.9 27.1 + - - +
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Residues in contact with ARG 520 (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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477A LEU* 3.6 50.7 + - + +
478A ASN* 4.9 4.4 + - - -
516A GLN* 2.9 62.6 + - - +
517A THR* 3.2 20.0 + - - +
519A THR* 1.3 77.0 - - - +
521A LEU* 1.3 57.6 + - - +
523A TYR* 3.2 8.4 + - - +
524A GLY* 2.9 26.3 + - - -
533A TRP* 3.4 57.6 - - + +
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Residues in contact with LEU 521 (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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303A VAL* 3.8 20.4 - - + +
306A LEU* 3.6 43.7 - - + -
307A ALA 4.5 3.4 - - - +
517A THR* 2.9 31.1 + - + +
518A VAL* 3.4 10.3 - - - +
520A ARG* 1.3 77.1 - - - +
522A LEU* 1.3 55.8 + - - +
524A GLY* 3.2 3.7 + - - -
525A PHE* 2.9 46.7 + - + -
533A TRP* 3.9 30.5 - - + -
534A PHE* 4.5 1.7 - - + -
570A ALA* 4.1 9.0 - - + -
574A LEU* 4.2 6.1 - - + -
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Residues in contact with LEU 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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299A VAL* 4.2 9.2 - - + -
300A ALA* 4.9 0.2 - - - -
303A VAL* 3.8 28.5 - - + -
463A ILE* 4.0 20.9 - - + -
465A VAL* 4.0 28.7 - - + -
467A TYR* 4.4 7.0 - - - +
481A THR* 5.9 0.2 - - + -
483A THR* 4.6 2.7 - - + -
484A ALA* 4.4 24.5 - - + -
487A LEU* 4.3 17.9 - - + -
518A VAL* 2.9 13.7 + - + +
519A THR* 3.4 9.0 - - - +
521A LEU* 1.3 77.1 - - - +
523A TYR* 1.3 53.8 + - - +
525A PHE* 3.2 1.8 + - - +
526A LEU* 2.6 42.3 + - + +
527A ILE* 5.0 1.3 - - - -
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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
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467A TYR* 4.2 7.1 + + - +
472A SER 3.6 9.2 + - - -
473A PRO 3.1 22.8 + - - -
474A GLU 4.3 1.1 - - - -
476A ASP* 3.2 35.2 - - + -
477A LEU* 3.4 37.9 - - + -
519A THR 2.9 12.2 + - - +
520A ARG* 3.3 11.4 - - - +
522A LEU* 1.3 76.4 - - - +
524A GLY* 1.3 60.9 + - - +
527A ILE* 3.0 49.8 + - + +
528A LYS* 2.9 34.1 + - + +
531A ASN* 3.3 36.5 + - + -
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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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477A LEU* 6.1 0.4 - - - -
520A ARG 2.9 13.6 + - - -
521A LEU 3.2 3.3 + - - -
523A TYR* 1.3 77.2 - - - +
525A PHE* 1.3 60.5 + - - +
528A LYS 2.8 23.2 - - - +
529A ALA* 3.6 3.1 - - - -
531A ASN* 3.8 4.7 - - - -
534A PHE* 3.3 40.2 - - - -
551A LEU* 4.3 4.2 + - - +
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Residues in contact with PHE 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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299A VAL* 3.8 19.1 - - + -
302A PHE* 3.4 32.1 - + - -
303A VAL* 3.7 19.5 - - + -
306A LEU* 4.2 5.2 - - + -
521A LEU* 2.9 46.5 + - + +
522A LEU 3.9 0.9 - - - +
524A GLY* 1.3 79.9 - - - +
526A LEU* 1.3 60.4 + - - +
527A ILE 3.6 0.2 - - - -
534A PHE* 3.6 23.8 - + - -
550A PRO* 3.1 23.4 - - - +
551A LEU* 3.4 21.5 + - + +
553A HIS* 3.7 23.7 + + - +
563A THR 4.7 1.1 - - - -
566A VAL* 4.0 13.9 - - + -
567A VAL* 3.9 14.4 - - + -
570A ALA* 5.1 1.3 - - + -
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Residues in contact with LEU 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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293A PRO* 3.6 29.6 - - + +
295A ALA* 3.4 24.9 - - + -
299A VAL* 3.5 26.5 - - + -
458A ASP 4.2 1.8 - - - +
459A THR* 3.4 26.6 - - - +
460A ALA* 5.1 5.7 - - - +
463A ILE* 3.8 20.0 - - + -
465A VAL* 5.3 4.0 - - + -
522A LEU* 2.6 23.2 + - + +
525A PHE* 1.3 76.8 - - - +
527A ILE* 1.3 70.0 + - + +
550A PRO* 4.2 13.3 - - + +
553A HIS* 5.1 1.8 - - - +
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Residues in contact with ILE 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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460A ALA* 5.1 8.3 - - + -
465A VAL* 4.1 13.2 - - + -
466A SER* 5.8 0.9 - - - -
467A TYR* 3.6 28.3 - - + -
476A ASP* 4.7 4.0 - - - +
522A LEU 4.6 1.1 - - - +
523A TYR* 3.0 54.8 + - + +
526A LEU* 1.3 90.6 - - + +
528A LYS* 1.3 65.2 + - + +
549A GLY 4.1 3.5 - - - +
550A PRO* 4.1 13.3 - - - +
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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