Contacts of the helix formed by residues 556 - 571 (chain F) in PDB entry 6X34
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 ALA 556 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516F LYS* 5.9 6.8 - - + +
519F VAL* 4.3 16.8 - - + -
520F ASN* 5.3 9.2 - - + +
523F TYR* 3.6 27.9 - - + -
554F LEU 3.6 2.2 + - - -
555F GLU* 1.3 75.6 - - + +
557F SER* 1.3 61.9 + - - +
558F SER 3.5 2.5 - - - +
559F GLY 4.4 3.4 - - - +
560F ILE* 3.4 22.0 + - - +
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Residues in contact with SER 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F LEU* 4.3 6.4 - - - +
553F ARG 4.1 9.4 - - - -
554F LEU 4.4 3.7 + - - -
555F GLU 4.5 0.7 - - - -
556F ALA* 1.3 74.7 - - - +
558F SER* 1.3 62.3 + - - +
559F GLY 3.3 2.2 - - - -
560F ILE* 3.4 7.5 + - - +
561F LEU* 2.9 29.6 + - - +
589F LEU* 4.5 10.5 - - - +
593F HIS* 3.7 34.3 - - - -
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Residues in contact with SER 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556F ALA* 3.5 0.6 - - - +
557F SER* 1.3 78.8 - - - +
559F GLY* 1.3 56.6 + - - +
561F LEU* 3.3 11.9 + - - +
562F GLU* 2.9 30.5 + - - +
598F LYS* 6.0 2.6 - - - +
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Residues in contact with GLY 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523F TYR* 4.4 20.2 - - - -
527F ALA* 5.0 1.2 - - - +
556F ALA* 4.2 5.9 + - - +
557F SER 3.3 0.6 - - - -
558F SER* 1.3 80.2 - - - +
560F ILE* 1.3 57.7 + - - +
562F GLU* 3.3 10.7 + - - +
563F VAL* 2.9 35.7 + - - +
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Residues in contact with ILE 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523F TYR* 3.6 42.8 - - + +
546F TRP* 6.3 2.0 - - + -
547F LEU* 3.9 26.4 - - + +
550F LYS* 4.3 19.7 - - + +
551F LEU* 3.6 35.0 - - + +
556F ALA 3.4 17.9 - - - +
557F SER* 3.4 6.4 + - - +
559F GLY* 1.3 74.3 - - - +
561F LEU* 1.3 57.7 + - - +
563F VAL* 3.3 8.5 + - + +
564F LEU* 2.9 28.6 + - + +
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Residues in contact with LEU 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F LEU* 4.4 6.9 - - + +
557F SER 2.9 17.9 + - - +
558F SER* 3.6 12.3 - - - +
560F ILE* 1.3 78.0 - - - +
562F GLU* 1.3 58.3 + - - +
564F LEU* 3.3 9.0 + - + +
565F TYR* 2.9 28.7 + - + +
586F ILE* 5.7 2.9 - - + -
589F LEU* 4.4 15.0 - - + -
596F ASN* 4.7 9.0 - - + -
598F LYS* 3.7 27.4 - - + +
599F VAL* 3.7 35.9 - - + -
602F VAL* 4.0 20.4 - - + -
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Residues in contact with GLU 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524F GLU* 6.2 0.2 - - - -
527F ALA* 4.5 12.2 - - + +
531F ARG* 2.5 33.8 + - - +
558F SER 2.9 17.9 + - - +
559F GLY* 3.7 8.4 - - - +
561F LEU* 1.3 76.3 - - - +
563F VAL* 1.3 57.4 + - - +
565F TYR* 3.3 12.1 + - + +
566F CYS* 2.9 28.9 + - + +
598F LYS* 6.5 0.4 - - - -
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Residues in contact with VAL 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523F TYR* 4.2 5.2 - - + +
526F LEU* 3.6 34.5 - - + -
527F ALA* 3.6 22.0 - - + +
530F ILE* 5.4 7.9 - - + +
540F PHE* 5.2 7.4 - - + -
547F LEU* 4.3 22.2 - - + -
559F GLY 2.9 23.2 + - - +
560F ILE* 3.6 11.4 - - + +
561F LEU 3.3 0.2 - - - -
562F GLU* 1.3 76.8 - - - +
564F LEU* 1.3 57.1 + - - +
566F CYS* 3.2 5.4 + - - +
567F VAL* 2.9 31.2 + - + +
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Residues in contact with LEU 564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544F LEU* 5.2 5.6 - - + -
547F LEU* 3.8 26.4 - - + +
548F VAL* 5.0 9.6 - - + -
551F LEU* 4.1 14.8 - - + -
560F ILE* 2.9 17.2 + - + +
561F LEU* 3.8 8.5 - - + +
563F VAL* 1.3 77.4 - - - +
565F TYR* 1.3 63.8 + - - +
567F VAL* 3.3 14.8 - - + +
568F LEU* 3.2 47.4 - - + +
586F ILE* 3.6 31.4 - - + -
602F VAL* 4.3 10.5 - - + -
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Residues in contact with TYR 565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561F LEU* 2.9 18.7 + - + +
562F GLU* 3.3 13.0 + - + +
564F LEU* 1.3 78.0 - - - +
566F CYS* 1.3 64.1 + - + +
567F VAL 3.7 0.2 + - - -
568F LEU* 3.7 6.8 + - - +
569F ILE* 3.4 30.2 + - + +
598F LYS* 4.8 4.3 - - + +
601F ASP* 3.6 34.7 - - + +
602F VAL* 3.6 30.2 - - + +
605F SER* 4.9 9.7 + - - -
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Residues in contact with CYS 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527F ALA* 4.7 3.8 - - + +
530F ILE* 4.8 10.5 - - + +
531F ARG* 3.5 59.5 - - - +
532F GLY 5.1 0.7 - - - -
537F CYS* 5.4 0.5 - - - +
562F GLU 2.9 16.8 + - - +
563F VAL* 3.2 5.6 + - - +
565F TYR* 1.3 80.6 - - + +
567F VAL* 1.3 61.6 + - - +
568F LEU 3.3 0.2 - - - -
569F ILE* 3.3 23.5 + - - +
570F GLU* 3.8 11.1 + - - +
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Residues in contact with VAL 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530F ILE* 5.0 8.7 - - + +
537F CYS* 4.2 26.1 - - + +
540F PHE* 4.1 24.5 - - + -
544F LEU* 5.5 1.3 - - + -
547F LEU* 4.4 8.5 - - + -
563F VAL* 2.9 18.4 + - + +
564F LEU* 3.3 33.9 - - + +
566F CYS* 1.3 77.6 - - - +
568F LEU* 1.3 68.2 + - + +
569F ILE 3.4 1.1 + - - -
570F GLU 4.6 0.4 - - - -
571F SER* 3.7 18.9 + - - +
574F VAL* 4.3 20.7 - - + +
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Residues in contact with LEU 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544F LEU* 6.0 0.4 - - + -
564F LEU* 3.2 37.8 + - + +
565F TYR* 3.7 2.7 + - - +
566F CYS 3.3 0.4 - - - -
567F VAL* 1.3 82.5 - - + +
569F ILE* 1.3 58.0 + - - +
571F SER 4.7 7.9 - - - +
572F PRO* 5.4 3.9 - - - +
574F VAL* 3.7 35.2 - - + -
575F LEU* 4.9 4.9 - - + +
578F ILE* 5.4 1.3 - - + -
602F VAL* 4.0 20.6 - - + -
605F SER* 3.7 29.2 + - - +
606F LEU* 3.7 34.8 - - + +
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Residues in contact with ILE 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F TYR* 3.4 29.6 + - + +
566F CYS* 3.3 24.2 - - - +
568F LEU* 1.3 80.0 - - - +
570F GLU* 1.3 71.4 + - + +
571F SER 3.7 1.3 - - - -
572F PRO* 5.4 1.2 - - - +
605F SER* 4.9 14.4 - - - -
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Residues in contact with GLU 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530F ILE 5.9 0.7 - - - +
532F GLY 5.9 4.9 - - - +
533F ASN 4.7 5.2 - - - +
534F ARG* 5.2 16.5 + - + +
537F CYS* 3.7 23.6 - - + -
566F CYS* 3.8 11.3 + - - +
567F VAL 4.5 0.6 + - - +
569F ILE* 1.3 86.8 - - + +
571F SER* 1.3 60.0 + - - +
572F PRO* 3.9 6.3 - - - +
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Residues in contact with SER 571 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F ARG* 5.0 12.8 - - - +
537F CYS* 4.0 31.5 + - - +
538F ALA* 4.6 4.7 + - - -
567F VAL 3.7 14.2 + - - +
568F LEU* 4.7 3.9 - - - -
569F ILE 5.0 2.2 - - - -
570F GLU* 1.3 80.5 - - - +
572F PRO* 1.3 60.8 - - - +
573F GLU* 3.2 29.5 + - - +
574F VAL* 3.9 12.5 + - - +
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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
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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