Contacts of the helix formed by residues 597 - 615 (chain B) in PDB entry 6IEH
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 597 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B GLN* 5.8 2.2 - - - +
593B GLN 3.0 17.9 + - - +
594B HIS* 3.4 6.7 + - - +
595B TYR 3.3 0.4 - - - -
596B ARG* 1.3 75.3 - - - +
598B ILE* 1.3 62.3 + - - +
599B PRO* 3.4 2.0 - - - -
600B GLY* 3.4 12.0 + - - +
601B VAL* 3.5 17.2 + - + +
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Residues in contact with ILE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B HIS* 3.5 20.3 + - + +
595B TYR* 3.4 13.4 + - + +
596B ARG 3.3 0.6 - - - -
597B ALA* 1.3 72.5 - - - +
599B PRO* 1.3 79.2 - - + +
601B VAL* 3.1 20.7 + - + +
602B VAL* 3.2 23.4 + - + +
838B GLU 5.4 3.1 - - - +
839B LEU* 5.5 2.0 - - - -
842B ALA* 2.7 58.6 - - + +
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Residues in contact with PRO 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B TYR 3.9 3.4 - - - +
596B ARG* 3.3 20.6 - - - +
597B ALA 3.4 0.2 - - - -
598B ILE* 1.3 101.0 - - + +
600B GLY* 1.3 59.0 + - - +
602B VAL* 3.7 8.6 + - + +
603B GLU* 3.3 20.1 + - - +
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Residues in contact with GLY 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ALA* 3.4 8.5 + - - +
598B ILE 3.2 0.6 - - - -
599B PRO* 1.3 79.2 - - - +
601B VAL* 1.3 58.9 + - - +
602B VAL 3.2 0.4 - - - -
603B GLU* 3.2 7.3 + - - +
604B LYS* 2.8 30.0 + - - +
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Residues in contact with VAL 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ALA* 3.5 17.0 + - + +
598B ILE* 3.1 15.1 + - + +
600B GLY* 1.3 76.1 - - - +
602B VAL* 1.3 59.9 + - - +
604B LYS* 3.4 6.2 + - - +
605B VAL* 3.0 29.9 + - + +
835B ALA* 3.5 31.6 - - + +
838B GLU* 4.2 13.2 - - + +
839B LEU* 3.9 21.3 - - + +
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Residues in contact with VAL 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ILE* 3.2 24.2 + - + +
599B PRO* 3.8 9.2 - - + +
601B VAL* 1.3 77.2 - - + +
603B GLU* 1.3 62.1 + - - +
605B VAL* 3.2 9.8 + - + +
606B LYS* 3.2 21.5 + - - +
839B LEU* 5.4 9.0 - - + -
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Residues in contact with GLU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B PRO 3.3 12.7 + - - +
600B GLY* 3.2 11.1 + - - +
602B VAL* 1.3 76.6 - - - +
604B LYS* 1.3 65.0 + - - +
606B LYS* 3.5 5.5 + - - +
607B ASN* 3.2 25.1 + - - +
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Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B GLY 2.8 16.3 + - - +
601B VAL* 3.7 8.5 - - - +
602B VAL 3.2 0.2 - - - -
603B GLU* 1.3 75.8 - - - +
605B VAL* 1.3 63.1 + - - +
607B ASN* 4.2 3.9 - - - +
608B SER* 3.0 27.8 + - - +
835B ALA* 5.2 8.3 - - + -
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Residues in contact with VAL 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B VAL* 3.0 20.9 + - + +
602B VAL* 3.5 9.9 - - + +
603B GLU 3.2 0.2 - - - -
604B LYS* 1.3 76.6 - - - +
606B LYS* 1.3 57.7 + - - +
608B SER* 3.2 5.2 + - - -
609B GLU* 2.7 51.7 + - + +
832B ILE* 4.4 7.9 - - + -
835B ALA* 3.7 31.0 - - + +
836B LYS* 4.3 20.9 - - + +
839B LEU* 5.4 3.1 - - + -
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Residues in contact with LYS 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B VAL* 3.2 13.1 + - - +
603B GLU* 4.0 6.1 - - - +
604B LYS 3.3 0.2 - - - -
605B VAL* 1.3 80.8 - - - +
607B ASN* 1.3 63.4 + - - +
609B GLU* 3.6 21.5 - - - +
610B GLU* 4.1 8.1 - - - -
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Residues in contact with ASN 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLU 3.2 15.6 + - - +
604B LYS* 4.2 4.0 - - - +
606B LYS* 1.3 76.9 + - - +
608B SER* 1.3 62.2 + - - +
610B GLU* 3.4 8.5 + - - +
611B GLN* 3.2 27.0 + - + +
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Residues in contact with SER 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B LYS* 3.0 20.7 + - - +
605B VAL* 3.6 3.8 - - - -
607B ASN* 1.3 78.5 - - - +
609B GLU* 1.3 62.4 + - - +
611B GLN* 3.2 10.3 + - - +
612B TYR* 3.2 17.0 + - - +
828B ILE* 4.0 16.2 - - - +
831B ASP* 4.6 9.9 - - - +
832B ILE* 3.7 27.9 - - - +
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Residues in contact with GLU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B VAL* 2.7 42.4 + - + +
606B LYS* 3.9 14.5 - - - +
607B ASN 3.2 0.2 - - - -
608B SER* 1.3 73.8 - - - +
610B GLU* 1.3 63.0 + - - +
612B TYR* 3.2 18.3 + - - +
613B ASN* 3.3 14.4 + - - +
832B ILE* 4.0 24.4 - - + +
836B LYS* 5.0 5.4 - - - +
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Residues in contact with GLU 610 (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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606B LYS 4.1 4.9 - - - -
607B ASN* 3.5 17.4 - - - +
609B GLU* 1.3 76.6 - - - +
611B GLN* 1.3 64.2 + - + +
613B ASN* 3.3 14.5 + - - +
614B LYS* 2.8 30.4 + - + +
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Residues in contact with GLN 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ASN 3.2 15.2 + - - +
608B SER* 3.3 14.1 - - - +
610B GLU* 1.3 82.0 - - - +
612B TYR* 1.3 62.8 - - - +
614B LYS* 3.8 10.5 - - - +
615B ILE* 3.1 37.2 + - - +
828B ILE* 4.1 18.6 - - + +
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Residues in contact with TYR 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B SER 3.2 8.2 + - - +
609B GLU* 3.3 11.2 - - - +
611B GLN* 1.3 79.6 - - - +
613B ASN* 1.3 67.1 + - - +
615B ILE* 3.5 9.3 - - - +
616B VAL* 2.9 26.7 + - + +
825B LYS* 2.8 64.7 + - + +
826B ALA* 5.5 0.2 - - - -
828B ILE* 4.4 9.3 - - + +
829B ALA* 4.1 22.0 - - + +
832B ILE* 4.3 13.9 - - + -
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Residues in contact with ASN 613 (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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609B GLU* 3.3 15.3 + - - +
610B GLU* 3.7 16.5 + - - +
611B GLN 3.2 0.6 - - - -
612B TYR* 1.3 86.8 - - - +
614B LYS* 1.3 66.0 + - - +
616B VAL* 3.0 21.7 + - - +
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Residues in contact with LYS 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B GLU* 2.8 19.6 + - + +
611B GLN* 3.8 15.5 - - - +
612B TYR 3.4 0.2 - - - -
613B ASN* 1.3 77.9 - - - +
615B ILE* 1.3 61.5 + - + +
616B VAL 3.3 1.9 + - - -
617B ILE* 4.7 6.2 - - - +
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Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B GLN* 3.1 29.3 + - - +
612B TYR* 3.5 5.2 - - - +
614B LYS* 1.3 80.0 - - + +
616B VAL* 1.3 58.7 + - - +
617B ILE* 2.8 12.7 + - - +
618B PRO* 3.6 6.9 - - + +
821B LEU* 4.6 23.2 - - + +
824B LYS* 5.3 5.4 - - + -
825B LYS* 2.2 58.8 - - + +
828B ILE* 4.4 8.3 - - + -
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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
------------------------------------------------------------
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