Contacts of the helix formed by residues 584 - 599 (chain F) in PDB entry 3IYD
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 ARG 584 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572F THR* 4.0 27.4 - - + +
573F LEU* 4.8 17.3 - - + +
576F VAL* 3.7 9.6 - - + +
583F THR* 1.3 83.9 - - - +
585F GLU* 1.3 62.0 + - + +
586F ARG 3.6 0.4 - - - -
587F ILE* 3.4 22.3 - - - +
588F ARG* 5.8 0.2 - - - +
44I T 6.3 1.8 - - + -
45I T 5.2 14.1 + - - +
51J T 4.1 27.4 + - - +
52J G 5.9 0.9 - - - +
53J T 5.4 5.0 - - - +
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Residues in contact with GLU 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582F VAL* 6.5 0.2 - - + -
583F THR* 3.3 6.3 + - - +
584F ARG* 1.3 78.7 - - - +
586F ARG* 1.3 60.9 + - - +
587F ILE 3.0 8.6 + - - -
588F ARG* 3.4 18.5 + - - +
589F GLN* 2.9 34.3 + - - +
43I T 3.1 35.6 - - + +
44I T 3.3 41.7 - - + +
53J T 5.1 5.1 - - - +
54J A 4.1 17.2 + - - +
55J A 4.7 4.0 + - - -
56J A 5.2 2.8 - - - +
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Residues in contact with ARG 586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F ARG* 5.2 8.5 - - - +
555F GLU* 4.0 14.3 + - - +
581F ASP* 4.5 3.2 + - - -
582F VAL* 3.5 38.0 - - + +
583F THR 4.3 2.6 + - - -
585F GLU* 1.3 87.2 + - - +
587F ILE* 1.3 60.7 + - - +
588F ARG 3.0 2.7 - - - -
589F GLN* 3.6 20.0 - - - +
590F ILE* 2.8 66.2 + - + +
41I G 3.0 35.8 + - - -
42I C 3.3 46.6 + - + -
43I T 4.4 2.7 - - + -
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Residues in contact with ILE 587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558F VAL* 6.3 4.5 - - + -
570F ASP* 5.4 1.3 - - - +
572F THR* 4.3 10.8 - - + +
575F GLU* 3.4 46.4 - - + +
576F VAL* 4.2 9.2 - - + -
579F GLN* 5.5 4.9 - - - +
582F VAL* 6.2 0.2 - - + -
583F THR 4.0 10.5 - - - +
584F ARG* 3.4 34.3 - - + +
585F GLU 3.0 1.2 - - - -
586F ARG* 1.3 78.3 - - - +
588F ARG* 1.3 57.8 + - + +
590F ILE* 5.5 1.6 - - + -
591F GLU* 3.2 30.7 - - - +
52J G 4.4 26.2 - - + +
53J T 4.7 0.7 + - - -
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Residues in contact with ARG 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584F ARG 4.8 0.2 + - - -
585F GLU* 3.4 11.2 + - - +
586F ARG 3.0 0.2 - - - -
587F ILE* 1.3 80.4 - - + +
589F GLN* 1.3 79.7 + - - +
590F ILE 3.6 0.2 - - - -
591F GLU* 3.9 3.0 - - - +
592F ALA* 3.2 37.5 + - + +
52J G 4.4 5.8 - - + -
53J T 3.2 58.9 + - + +
54J A 2.9 69.2 + - - +
56J A 5.9 3.1 - - - +
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Residues in contact with GLN 589 (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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585F GLU* 2.9 30.9 + - - +
586F ARG* 3.3 24.6 + - + +
588F ARG* 1.3 93.4 - - - +
590F ILE* 1.3 57.2 + - - +
592F ALA* 3.1 2.9 + - - +
593F LYS* 2.8 56.3 + - + +
40I G 5.5 2.9 - - - +
41I G 4.2 8.1 + - - +
42I C 2.9 34.2 + - - +
56J A 6.3 1.1 - - - -
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Residues in contact with ILE 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F ARG* 5.8 0.9 - - + -
555F GLU* 3.7 35.7 - - + +
558F VAL* 3.8 36.1 - - + -
559F LEU* 4.0 1.3 - - + -
579F GLN* 4.0 17.0 - - - +
586F ARG* 2.8 69.8 + - + +
587F ILE* 5.5 1.8 - - + -
589F GLN* 1.3 72.1 - - + +
591F GLU* 1.3 58.9 + - + +
593F LYS* 3.5 7.1 + - - +
594F ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 591 (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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558F VAL* 5.4 5.1 - - + +
559F LEU* 3.9 28.8 - - + +
569F THR* 4.7 2.8 + - - -
570F ASP* 3.0 28.1 - - - +
575F GLU* 4.4 9.2 - - - +
586F ARG 4.3 0.2 + - - -
587F ILE* 3.2 22.5 - - - +
588F ARG 3.7 6.5 + - - +
589F GLN 3.2 0.6 - - - -
590F ILE* 1.3 79.1 - - + +
592F ALA* 1.3 57.0 + - - +
594F ALA* 3.2 3.5 + - - +
595F LEU* 2.9 37.7 + - + +
52J G 5.1 0.6 - - - +
53J T 3.6 22.6 + - - +
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Residues in contact with ALA 592 (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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588F ARG* 3.2 39.0 + - - +
589F GLN 3.1 1.7 + - - +
591F GLU* 1.3 76.3 - - - +
593F LYS* 1.3 64.9 + - + +
595F LEU* 3.1 30.1 + - + +
596F ARG* 3.5 27.9 + - - +
54J A 5.1 3.8 - - - +
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Residues in contact with LYS 593 (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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264A VAL* 4.6 20.2 - - - +
555F GLU* 3.4 29.6 - - - +
589F GLN* 2.8 43.1 + - + +
590F ILE* 3.8 4.0 - - - +
592F ALA* 1.3 73.5 - - + +
594F ALA* 1.3 57.9 + - - +
596F ARG* 3.2 31.7 + - - +
597F LYS* 3.2 30.6 + - - +
40I G 4.7 26.2 + - + -
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Residues in contact with ALA 594 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F LEU* 6.5 0.7 - - + -
555F GLU* 4.3 11.4 + - + +
556F ALA* 5.9 0.9 - - - -
559F LEU* 3.7 27.6 - - + -
590F ILE 2.9 18.7 + - - +
591F GLU 3.5 4.7 - - - +
593F LYS* 1.3 77.1 - - - +
595F LEU* 1.3 59.9 + - - +
597F LYS* 2.8 28.7 + - + +
598F LEU* 3.0 21.7 + - + +
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Residues in contact with LEU 595 (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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901C LEU* 6.2 2.2 - - + -
559F LEU* 5.3 8.1 - - + -
591F GLU* 2.9 28.1 + - + +
592F ALA* 3.1 19.4 + - + +
594F ALA* 1.3 75.0 - - - +
596F ARG* 1.3 57.0 + - + +
598F LEU* 2.9 32.8 + - + +
599F ARG* 2.7 25.6 + - - +
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Residues in contact with ARG 596 (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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264A VAL* 5.9 6.5 - - + +
268A ASN* 6.1 2.0 - - - +
592F ALA* 3.5 21.0 + - - +
593F LYS* 3.2 51.1 + - - +
594F ALA 3.3 0.6 - - - -
595F LEU* 1.3 79.2 - - + +
597F LYS* 1.3 59.4 + - + +
599F ARG* 3.5 35.6 - - - +
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Residues in contact with LYS 597 (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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264A VAL* 3.7 31.8 - - + +
551F LEU* 3.7 32.9 - - + +
552F THR* 3.1 31.9 + - - +
555F GLU* 2.9 31.4 + - + +
593F LYS* 3.2 19.1 - - - +
594F ALA* 2.8 16.2 + - + +
596F ARG* 1.3 75.4 - - + +
598F LEU* 1.3 58.9 + - + +
599F ARG 3.0 9.1 + - - -
600F HIS* 3.2 23.3 + - - +
601F PRO* 3.7 1.7 - - - +
40I G 6.2 2.4 - - - -
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Residues in contact with LEU 598 (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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901C LEU* 3.6 29.3 - - + +
544F THR* 4.2 18.4 - - + -
548F LEU* 5.4 11.0 - - + -
559F LEU* 5.6 5.4 - - + -
594F ALA* 3.0 36.6 + - + +
595F LEU* 2.9 19.8 + - + +
597F LYS* 1.3 77.2 - - + +
599F ARG* 1.3 59.6 + - - +
600F HIS 3.1 1.6 - - - -
601F PRO* 3.1 23.0 - - + +
605F GLU* 4.9 1.6 - - - +
607F LEU* 3.8 33.2 - - + -
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Residues in contact with ARG 599 (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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258A ASP* 2.8 23.1 - - - +
271A LYS* 4.6 9.9 - - - +
897C PRO 4.7 3.4 + - - -
900C LYS* 3.7 13.7 + - - +
901C LEU* 3.4 55.4 - - - +
904C ALA* 3.5 28.3 - - + +
905C ILE* 3.2 21.1 - - + +
595F LEU* 2.7 43.6 + - - +
596F ARG* 3.5 30.6 - - - +
597F LYS 3.0 0.6 - - - -
598F LEU* 1.3 77.4 - - - +
600F HIS* 1.3 62.6 + - - +
601F PRO 3.5 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
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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