Contacts of the helix formed by residues 554 - 563 (chain A) in PDB entry 3FO5
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 VAL 554 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A 1PE 3.9 32.1 - - - +
479A LEU* 3.8 25.1 - - + -
486A GLN* 3.4 27.1 - - - +
488A PHE* 5.0 0.2 - - + -
548A ASN* 5.8 0.2 - - - +
551A THR* 2.9 38.0 + - + +
553A GLY* 1.3 77.9 - - - +
555A LEU* 1.3 64.8 + - - +
556A ASN 3.3 2.5 - - - -
557A TYR* 3.1 15.2 + - + +
558A VAL* 3.1 24.8 + - + +
595A GOL 4.1 0.7 - - - -
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Residues in contact with LEU 555 (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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361A ASP* 4.7 11.9 - - - +
364A TYR* 3.3 46.0 - - + +
424A LEU* 4.5 5.8 - - + -
552A PRO* 3.3 14.3 + - + +
553A GLY 3.5 1.0 - - - -
554A VAL* 1.3 77.7 - - - +
556A ASN* 1.3 58.3 + - - +
558A VAL* 3.2 3.4 + - + +
559A THR* 2.9 44.8 + - + +
595A GOL 3.2 37.1 + - - +
498B CYS* 3.8 20.2 - - + -
500B ASN* 4.4 6.6 - - - +
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Residues in contact with ASN 556 (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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357A LYS* 2.8 27.8 + - - +
361A ASP* 3.9 7.1 - - - +
480A GLY* 5.3 4.8 + - - +
554A VAL 3.3 1.0 - - - -
555A LEU* 1.3 78.2 - - - +
557A TYR* 1.3 54.5 + - - +
559A THR* 3.1 15.0 + - - -
560A THR* 2.7 35.8 + - - -
396B LYS* 3.0 33.5 + - - +
500B ASN* 5.3 0.2 - - - +
502B ASP* 3.9 20.8 + - - +
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Residues in contact with TYR 557 (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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2A 1PE 4.1 11.4 - - - -
454A LYS* 4.9 1.4 - - - +
455A HIS* 2.5 40.7 + + - -
479A LEU* 3.9 38.6 - - + -
554A VAL* 3.1 12.2 + - + +
556A ASN* 1.3 79.2 - - - +
558A VAL* 1.3 63.9 + - + +
560A THR* 3.4 6.5 + - - -
561A ASN* 2.8 40.3 + - - -
568A GLU* 3.1 52.0 + - + +
569A PHE* 3.4 25.6 - + - -
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Residues in contact with VAL 558 (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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2A 1PE 5.2 0.7 - - - -
424A LEU* 3.8 25.1 - - + -
426A PHE* 3.8 34.3 - - + -
554A VAL* 3.1 21.8 + - + +
555A LEU* 3.5 7.6 - - + +
557A TYR* 1.3 74.1 - - + +
559A THR* 1.3 60.2 + - - +
561A ASN* 3.4 1.0 + - - +
562A VAL* 2.8 40.6 + - + +
569A PHE* 3.9 12.6 - - + -
595A GOL 3.7 27.6 - - - +
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Residues in contact with THR 559 (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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357A LYS* 3.4 12.1 - - - -
360A LEU* 3.8 28.7 - - + +
361A ASP* 2.6 30.9 + - - +
424A LEU* 3.8 21.5 - - + -
555A LEU* 2.9 32.5 + - + +
556A ASN 3.1 13.0 + - - -
558A VAL* 1.3 72.3 - - - +
560A THR* 1.3 56.5 + - - +
562A VAL* 4.1 1.2 - - - +
563A ALA* 2.8 34.8 + - - +
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Residues in contact with THR 560 (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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357A LYS* 3.1 22.0 - - - -
556A ASN* 2.7 29.2 + - - -
557A TYR* 3.6 8.6 - - - -
558A VAL 3.3 0.2 - - - -
559A THR* 1.3 75.1 + - - +
561A ASN* 1.3 61.2 + - - +
563A ALA* 3.9 1.2 - - - +
564A GLY 3.3 2.8 + - - -
565A LEU* 2.9 35.3 + - + +
566A SER* 3.3 21.5 + - - -
568A GLU* 5.6 0.7 - - - +
389B TYR* 3.2 29.8 - - + +
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Residues in contact with ASN 561 (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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415A LEU* 4.1 10.5 - - + +
557A TYR* 2.8 52.6 + - - +
560A THR* 1.3 74.5 - - - +
562A VAL* 1.3 61.0 + - - +
564A GLY* 2.9 21.1 + - - -
566A SER* 3.4 18.3 + - - +
567A SER* 3.7 0.3 - - - -
568A GLU* 3.0 33.4 + - - -
569A PHE* 3.1 44.3 + - + +
570A TYR* 6.0 0.2 - - - -
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Residues in contact with VAL 562 (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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356A LYS* 3.8 20.3 + - - +
360A LEU* 3.7 21.5 - - + -
407A SER* 4.7 7.0 - - - +
408A SER* 5.4 2.6 + - - -
415A LEU* 4.2 15.1 - - + +
417A THR* 3.6 35.9 - - + -
419A GLU* 6.1 0.2 - - - +
424A LEU* 4.7 7.2 - - + -
426A PHE* 4.4 9.6 - - + -
558A VAL* 2.8 40.4 + - + +
559A THR* 4.1 3.1 - - - +
561A ASN* 1.3 72.1 - - - +
563A ALA* 1.3 60.2 + - - +
564A GLY* 3.2 1.4 + - - -
569A PHE* 4.6 4.5 - - + -
596A TCE 5.9 0.3 - - - -
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Residues in contact with ALA 563 (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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353A SER* 3.1 32.1 + - - +
356A LYS* 3.9 15.3 - - + -
357A LYS* 3.6 21.8 - - + +
360A LEU* 5.0 0.4 - - + -
559A THR 2.8 19.8 + - - +
560A THR 3.9 4.3 - - - +
562A VAL* 1.3 77.2 - - - +
564A GLY* 1.3 57.4 + - - +
565A LEU* 4.5 3.1 - - + +
596A TCE 3.0 23.6 - - - +
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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