Contacts of the helix formed by residues 557 - 573 (chain B) in PDB entry 1F1J
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 GLU 557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B LEU* 1.3 75.6 - - - +
558B ILE* 1.3 87.0 + - - +
559B MET* 2.7 38.6 + - - +
560B GLN* 2.9 36.9 + - + +
561B ILE* 3.1 8.8 + - - +
595B LEU* 5.2 0.5 - - - +
597B LYS 4.5 1.2 - - - +
598B GLU* 3.4 37.9 - - + +
599B LEU 2.9 31.3 + - - +
600B TYR* 3.5 19.0 - - + +
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Residues in contact with ILE 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 5.1 1.8 - - + -
482B PHE* 4.7 13.5 - - + -
520B LEU* 4.6 10.8 - - + -
545B LEU* 6.4 0.2 - - + -
549B LEU* 5.5 2.2 - - + -
556B LEU 3.8 0.8 + - - -
557B GLU* 1.3 93.9 - - - +
559B MET* 1.3 63.1 + - + +
561B ILE* 3.2 16.9 + - + -
562B LEU* 2.9 50.2 + - + +
595B LEU* 4.0 18.6 - - + -
599B LEU* 3.0 38.1 + - + +
601B PHE* 4.1 25.5 - - + -
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Residues in contact with MET 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MET* 3.8 58.3 - - + -
263A THR* 5.0 6.3 - - - +
293A SER* 4.7 7.2 - - - -
520B LEU* 4.1 25.4 - - - -
557B GLU* 2.7 25.7 + - - +
558B ILE* 1.3 74.3 - - + +
560B GLN* 1.3 49.7 + - + +
562B LEU* 3.3 3.5 + - + +
563B THR* 2.8 45.7 + - - +
591B VAL* 3.8 28.7 - - + -
593B SER* 4.4 8.1 - - - +
595B LEU* 5.6 1.1 - - + -
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Residues in contact with GLN 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.8 36.4 + - + +
555B ASP 5.1 0.2 - - - +
556B LEU* 3.7 31.2 - - + +
557B GLU* 2.9 39.2 + - + +
559B MET* 1.3 75.1 - - + +
561B ILE* 1.3 65.3 + - - +
563B THR* 4.0 5.2 - - - -
564B ARG* 3.0 34.3 + - - +
600B TYR* 4.0 7.4 + - - -
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Residues in contact with ILE 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LEU* 4.8 4.7 - - + -
548B ILE* 3.8 22.3 - - + +
549B LEU* 3.9 34.8 - - + -
552B HIS 3.7 15.3 - - - +
553B GLY* 4.1 6.7 - - - +
556B LEU* 3.5 40.6 - - + +
557B GLU 3.1 7.0 + - - +
558B ILE* 3.5 21.1 - - + +
560B GLN* 1.3 77.1 - - - +
562B LEU* 1.3 58.8 + - + +
564B ARG* 3.0 7.4 + - - +
565B VAL* 2.9 36.7 + - + +
601B PHE* 4.9 3.8 - - + -
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 4.2 14.4 - - + -
520B LEU* 4.0 23.1 - - + -
522B ALA* 4.1 20.2 - - + -
541B PHE* 4.9 5.8 - - + -
545B LEU* 4.3 15.0 - - + -
558B ILE* 2.9 33.8 + - + +
559B MET* 3.9 6.7 - - + +
561B ILE* 1.3 73.9 - - + +
563B THR* 1.3 60.1 + - - +
565B VAL* 3.2 9.9 + - + +
566B ASN* 2.8 34.5 + - - +
591B VAL* 3.8 38.4 - - + -
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Residues in contact with THR 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 5.6 1.2 + - - -
259A MET* 5.1 5.4 - - - +
293A SER* 4.9 6.1 + - - -
295A LEU* 3.9 9.9 + - + +
296A THR 3.4 2.9 - - - +
297A LYS* 3.2 47.2 + - - +
298A GLU* 4.5 5.3 - - + +
559B MET* 2.8 36.3 + - - +
560B GLN* 4.0 6.3 - - - -
562B LEU* 1.3 72.5 - - - +
564B ARG* 1.3 59.9 + - + +
566B ASN* 3.0 12.3 + - - +
567B ASP* 2.9 27.0 + - - +
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Residues in contact with ARG 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.3 67.0 + - + +
296A THR 5.3 0.2 - - - -
298A GLU* 4.6 9.8 + - - +
548B ILE* 4.1 26.5 - - + +
552B HIS* 3.7 26.9 + - - -
556B LEU* 3.3 35.5 - - - +
560B GLN* 3.0 19.2 + - - +
561B ILE 3.0 9.0 + - - +
563B THR* 1.3 82.0 - - + +
565B VAL* 1.3 57.1 + - - +
567B ASP* 3.5 8.0 + - - +
568B ARG* 3.1 27.9 + - - +
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Residues in contact with VAL 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PHE* 3.9 34.1 - - + -
544B ALA* 4.2 5.4 - - + -
545B LEU* 3.9 38.4 - - + +
548B ILE* 3.8 20.2 - - + -
561B ILE* 2.9 24.9 + - + +
562B LEU* 3.4 12.1 - - + +
564B ARG* 1.3 75.4 - - - +
566B ASN* 1.3 65.4 + - - +
568B ARG* 3.1 5.1 + - - +
569B VAL* 3.0 31.9 + - + +
589B PRO* 4.9 0.4 - - + -
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Residues in contact with ASN 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER* 3.6 24.4 + - - -
294A MET* 3.8 4.0 - - - +
295A LEU 2.8 26.7 + - - +
296A THR* 4.2 1.3 - - - -
562B LEU 2.8 18.5 + - - +
563B THR* 3.1 11.5 - - - +
565B VAL* 1.3 76.5 - - - +
567B ASP* 1.3 58.4 + - - +
570B ALA* 3.0 32.4 + - - +
588B ILE* 3.7 9.7 - - + +
589B PRO* 3.0 41.1 - - - +
591B VAL* 4.2 11.1 - - - +
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Residues in contact with ASP 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 5.6 5.2 - - - -
296A THR* 3.1 38.9 - - - +
297A LYS* 3.5 22.8 + - - +
563B THR 2.9 10.1 + - - +
564B ARG* 3.8 8.3 - - - +
565B VAL 3.3 0.2 - - - -
566B ASN* 1.3 77.3 - - - +
568B ARG* 1.3 57.1 + - - +
570B ALA* 4.5 0.7 - - - -
571B ARG* 2.8 56.3 + - - +
572B HIS* 4.3 1.3 + - - -
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ALA* 3.7 27.1 - - + +
547B SER* 3.4 23.8 + - - -
548B ILE* 3.1 27.6 - - + +
564B ARG 3.1 17.6 + - - +
565B VAL* 3.1 5.8 + - - +
567B ASP* 1.3 75.2 - - - +
569B VAL* 1.3 61.7 + - - +
572B HIS* 2.8 58.4 + - + +
573B PHE* 3.5 10.5 - - - -
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Residues in contact with VAL 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B TRP* 4.2 16.5 - - + +
541B PHE* 4.2 11.0 - - - -
544B ALA* 3.8 17.9 - - + -
565B VAL* 3.0 21.7 + - + +
568B ARG* 1.3 77.0 - - - +
570B ALA* 1.3 64.5 + - - +
573B PHE* 3.3 30.1 + - - +
587B GLN* 3.9 42.3 + - + +
589B PRO* 3.7 25.4 - - + -
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Residues in contact with ALA 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS 4.0 0.4 - - - +
213A ILE* 6.4 0.2 - - + -
214A PRO* 3.7 25.9 - - + +
296A THR* 4.5 7.6 - - + -
566B ASN 3.0 20.5 + - - +
567B ASP* 4.2 2.2 - - - +
569B VAL* 1.3 79.2 - - - +
571B ARG* 1.3 57.1 + - + +
586B LYS* 2.7 37.9 + - - -
587B GLN 3.4 10.9 + - - -
588B ILE* 3.8 14.1 - - + -
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Residues in contact with ARG 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 2.8 37.6 + - - +
212A LYS 5.0 3.4 - - - -
213A ILE* 3.5 23.3 - - + +
296A THR* 5.0 6.5 + - - -
297A LYS* 4.6 16.7 - - - +
567B ASP* 2.8 46.0 + - - +
570B ALA* 1.3 79.5 - - + +
572B HIS* 1.3 81.8 + - + +
573B PHE 3.8 0.4 - - - -
586B LYS* 4.5 5.8 + - - +
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Residues in contact with HIS 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B ASP* 4.3 1.4 + - - -
568B ARG* 2.8 60.0 + - + +
571B ARG* 1.3 95.2 + - + +
573B PHE* 1.3 73.5 + - + +
586B LYS* 5.4 0.2 - - - -
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Residues in contact with PHE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B TRP* 3.3 75.5 - + + -
543B GLN* 3.6 29.6 - - + -
544B ALA* 4.3 8.3 - - + -
568B ARG* 3.5 20.4 - - - -
569B VAL* 3.3 30.7 + - - +
570B ALA 4.1 1.0 - - - +
572B HIS* 1.3 88.9 - - + +
574B GLU* 1.3 61.7 + - - +
586B LYS* 3.1 28.3 + - - +
587B GLN 5.2 0.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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