Contacts of the helix formed by residues 561 - 576 (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 THR 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASP* 3.8 7.2 - - - +
290A ASN* 5.6 2.1 + - - -
331A GLN* 4.3 3.4 - - - +
545A TYR* 4.8 10.0 - - - -
552A GLN 4.9 4.2 + - - +
554A TYR* 3.2 27.3 + - - +
556A ALA* 4.1 6.2 - - - +
558A SER* 3.6 20.5 + - - -
559A SER* 3.4 4.2 - - - +
560A PRO* 1.3 89.2 - - - +
562A ASN* 1.3 72.6 + - - +
563A THR* 3.8 9.9 - - - +
564A THR* 3.1 32.9 + - - +
565A TYR* 3.6 9.9 + - - +
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Residues in contact with ASN 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASN* 4.6 13.5 + - - -
545A TYR* 3.0 54.4 + - - +
551A LEU* 4.2 16.5 - - + +
552A GLN 5.1 8.9 - - - +
561A THR* 1.3 80.9 + - - +
563A THR* 1.3 64.0 + - - +
565A TYR* 3.8 3.3 + - - +
566A VAL* 3.2 26.0 + - - +
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Residues in contact with THR 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.2 11.4 - - + +
302A PHE* 4.7 0.4 - - + -
331A GLN* 3.6 24.5 - - - +
525A PHE* 4.7 0.6 - - + -
551A LEU* 3.8 15.1 - - - +
552A GLN 4.0 4.7 + - - -
553A HIS* 2.7 51.4 + - + +
561A THR* 3.2 9.6 + - - +
562A ASN* 1.3 79.9 - - - +
564A THR* 1.3 63.0 - - - +
566A VAL* 3.2 6.6 + - - +
567A VAL* 2.9 33.9 + - + +
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Residues in contact with THR 564 (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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254A TYR* 3.4 37.9 + - + +
256A VAL* 3.4 18.0 - - + +
282A LEU* 4.7 2.5 - - + -
331A GLN* 3.5 18.0 + - - +
560A PRO* 3.2 19.0 + - + -
561A THR* 3.1 19.6 + - - +
563A THR* 1.3 81.8 - - - +
565A TYR* 1.3 57.9 + - - +
567A VAL* 3.2 7.1 + - - +
568A GLN* 2.9 27.7 + - - +
627A LEU* 4.5 4.0 - - + -
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Residues in contact with TYR 565 (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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539A ARG* 4.8 9.5 + - - -
542A LEU* 3.3 39.5 - - + -
545A TYR* 3.7 33.2 - + + -
560A PRO* 3.4 43.9 - - + +
561A THR 3.6 5.2 + - - -
562A ASN 4.2 7.0 - - - +
563A THR 3.3 0.2 - - - -
564A THR* 1.3 78.5 - - - +
566A VAL* 1.3 59.1 + - + +
568A GLN* 3.2 21.9 + - - +
569A TYR* 2.9 40.1 + + - +
627A LEU* 4.3 12.8 - - + -
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Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A PHE* 4.0 5.8 - - + -
534A PHE* 3.1 47.3 - - + +
538A LEU* 4.4 15.9 - - + -
545A TYR* 5.3 4.7 - - + -
546A LEU* 3.3 27.6 - - + -
551A LEU* 3.8 9.4 - - + -
562A ASN 3.2 16.8 - - - +
563A THR 3.2 7.7 + - - +
565A TYR* 1.3 77.8 - - + +
567A VAL* 1.3 52.7 + - - +
569A TYR* 3.2 1.4 + - - +
570A ALA* 2.7 38.2 + - + +
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Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 3.2 37.0 - - + -
282A LEU* 3.6 20.2 - - + -
302A PHE* 3.2 38.6 - - + -
306A LEU* 4.4 5.8 - - + +
329A PHE* 4.4 7.6 - - + -
525A PHE* 3.9 7.4 - - + -
563A THR* 2.9 15.9 + - + +
564A THR* 3.4 8.3 - - - +
566A VAL* 1.3 78.1 - - - +
568A GLN* 1.3 52.9 + - - +
570A ALA* 3.8 5.2 - - - +
571A LEU* 2.7 37.4 + - - +
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Residues in contact with GLN 568 (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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256A VAL* 4.5 5.4 - - + -
564A THR 2.9 13.2 + - - +
565A TYR* 3.3 21.7 - - - +
567A VAL* 1.3 78.0 - - - +
569A TYR* 1.3 77.6 + - + +
571A LEU* 3.4 6.4 + - - +
572A ALA* 2.9 27.5 + - + +
601A GLU* 3.7 12.3 + - - -
625A ALA* 3.2 30.3 + - + +
626A ARG 4.1 3.3 - - - +
627A LEU* 3.3 46.3 - - + +
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Residues in contact with TYR 569 (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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537A ILE* 3.0 39.4 - - + +
538A LEU* 3.8 14.6 - - + -
539A ARG* 3.5 40.4 + - + +
542A LEU* 3.5 31.4 - - + +
565A TYR* 2.9 29.6 + + - +
566A VAL 4.0 2.0 - - - +
568A GLN* 1.3 94.9 + - + +
570A ALA* 1.3 58.8 + - - +
572A ALA* 3.2 10.6 + - + +
573A ASN 2.9 24.1 + - - -
603A SER* 3.8 31.1 - - - -
605A VAL* 5.3 3.6 - - + -
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Residues in contact with ALA 570 (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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306A LEU* 4.9 2.9 - - + -
521A LEU* 4.1 25.4 - - + -
525A PHE* 5.1 1.1 - - + -
533A TRP* 4.3 10.5 - - + -
534A PHE* 4.6 7.6 - - + -
537A ILE* 4.5 9.2 - - + +
566A VAL 2.7 22.9 + - - +
567A VAL* 3.8 5.6 - - - +
569A TYR* 1.3 71.9 - - - +
571A LEU* 1.3 57.8 + - - +
573A ASN* 3.2 7.0 + - - +
574A LEU* 2.9 37.2 + - + +
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Residues in contact with LEU 571 (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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256A VAL* 3.8 16.6 - - + -
257A TRP 4.6 1.8 - - - +
258A SER* 3.6 27.8 - - - +
306A LEU* 3.9 21.3 - - + +
309A ALA* 4.4 12.8 - - + -
327A PHE* 5.0 0.9 - - + -
329A PHE* 3.4 31.0 - - + -
567A VAL 2.7 22.8 + - - +
568A GLN* 3.5 5.8 - - + +
569A TYR 3.2 0.2 - - - -
570A ALA* 1.3 74.0 - - - +
572A ALA* 1.3 57.6 + - - +
574A LEU* 3.2 4.2 + - + +
575A THR* 2.9 49.9 + - + -
625A ALA* 4.4 9.0 - - + -
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Residues in contact with ALA 572 (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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537A ILE* 5.3 2.0 - - + -
568A GLN* 2.9 13.9 + - + +
569A TYR* 3.2 20.8 + - + +
571A LEU* 1.3 75.1 - - - +
573A ASN* 1.3 57.5 + - - +
575A THR* 3.8 2.5 - - - -
576A GLY* 2.6 36.2 + - - -
603A SER* 5.2 3.4 - - - +
621A VAL* 4.0 12.6 - - + +
623A SER* 3.2 33.0 - - - -
625A ALA* 4.6 1.1 - - - +
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Residues in contact with ASN 573 (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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310A GLU* 5.0 1.1 + - - +
533A TRP* 4.2 19.4 - - + +
536A SER 4.9 1.6 - - - +
537A ILE* 3.5 36.1 - - + +
569A TYR 2.9 12.7 + - - +
570A ALA 3.4 8.1 - - - +
572A ALA* 1.3 78.5 - - - +
574A LEU* 1.3 67.7 + - + +
576A GLY 3.8 10.4 - - - +
621A VAL* 5.0 12.1 - - - +
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Residues in contact with LEU 574 (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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306A LEU* 3.7 44.6 - - + +
310A GLU* 2.9 56.9 - - + +
313A GLN* 4.4 3.5 - - - +
517A THR* 4.3 8.7 - - + -
521A LEU* 4.2 13.9 - - + -
533A TRP* 3.8 29.2 - - + -
570A ALA 2.9 21.2 + - - +
571A LEU* 3.2 8.5 + - + +
573A ASN* 1.3 81.9 - - + +
575A THR* 1.3 67.1 + - - +
576A GLY 4.2 1.2 - - - +
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Residues in contact with THR 575 (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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258A SER* 3.8 20.6 + - - +
259A MET 4.7 2.7 - - - +
309A ALA* 4.5 13.9 - - + +
313A GLN* 3.1 49.5 - - - +
327A PHE* 5.5 2.7 - - + -
571A LEU* 2.9 34.6 + - + +
572A ALA* 3.4 2.6 + - - -
574A LEU* 1.3 73.8 - - - +
576A GLY* 1.3 72.0 + - - +
577A THR* 5.5 0.2 - - - +
623A SER 2.9 21.0 + - - -
624A THR* 5.5 1.1 - - - -
625A ALA* 4.9 0.2 - - - +
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Residues in contact with GLY 576 (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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572A ALA 2.6 24.9 + - - -
573A ASN 3.8 10.1 - - - +
574A LEU 4.2 1.4 - - - +
575A THR* 1.3 81.5 + - - +
577A THR* 1.3 65.2 + - - -
621A VAL* 4.5 2.9 - - - -
622A ARG* 3.2 18.6 - - - -
623A SER* 4.4 1.8 - - - -
624A THR* 5.6 1.3 - - - -
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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