Contacts of the helix formed by residues 592 - 607 (chain H) in PDB entry 4E2I
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 ILE 592 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H THR* 4.1 11.9 - - + +
365H PHE* 3.7 32.8 - - + -
366H ASN* 3.4 32.5 - - - +
369H LEU* 4.5 3.8 - - + -
588H PHE* 3.6 12.3 - - + -
589H ALA* 3.0 40.2 + - + +
591H SER* 1.3 81.2 + - - +
593H GLN* 1.3 58.6 + - - +
594H SER 3.0 2.9 - - - -
595H ARG* 2.8 27.9 + - + +
596H ILE* 3.0 24.9 + - + +
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Residues in contact with GLN 593 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585H VAL* 3.1 44.9 + - + +
586H ALA* 4.3 8.1 + - - +
588H PHE 3.6 9.2 + - - +
589H ALA 2.9 18.5 + - - +
590H GLN* 3.1 41.0 + - - +
591H SER 3.7 0.4 - - - -
592H ILE* 1.3 78.2 - - - +
594H SER* 1.3 58.7 + - - +
596H ILE* 3.5 3.8 + - - -
597H VAL* 3.1 30.5 + - - +
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Residues in contact with SER 594 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590H GLN 5.0 2.8 + - - -
591H SER 5.5 4.0 - - - -
592H ILE 3.0 2.1 - - - +
593H GLN* 1.3 79.9 - - - +
595H ARG* 1.3 57.9 + - - +
597H VAL* 4.1 6.1 + - - +
598H GLU* 3.1 27.9 + - - +
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Residues in contact with ARG 595 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ASN* 3.2 40.7 + - - +
369H LEU* 3.2 27.9 - - + +
370H ASP* 3.1 37.0 + - - +
373H ASP* 2.8 28.9 + - - -
592H ILE* 2.8 17.7 + - + +
594H SER* 1.3 79.6 - - - +
596H ILE* 1.3 65.2 + - - +
597H VAL 3.3 0.4 - - - -
598H GLU* 3.1 35.6 - - - +
599H TRP* 3.6 14.8 + - + +
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Residues in contact with ILE 596 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H PHE* 5.6 1.3 - - + -
369H LEU* 4.8 9.2 - - + -
576H LEU* 6.0 0.9 - - + -
580H ILE* 3.6 24.2 - - + +
585H VAL* 4.1 7.0 - - + -
588H PHE* 3.4 61.0 - - + -
592H ILE* 3.2 34.3 - - + +
593H GLN* 3.8 7.4 - - - +
595H ARG* 1.3 77.6 - - - +
597H VAL* 1.3 62.0 + - - +
598H GLU 3.3 0.2 + - - -
599H TRP 3.4 2.8 + - - -
600H LYS* 3.2 39.4 + - - +
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Residues in contact with VAL 597 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585H VAL* 3.7 23.1 - - + -
593H GLN 3.1 18.1 + - - +
594H SER* 4.3 7.0 - - - +
595H ARG 3.3 0.2 - - - -
596H ILE* 1.3 73.6 - - - +
598H GLU* 1.3 65.0 + - - +
600H LYS* 3.1 20.6 + - + +
601H GLU* 3.1 29.6 + - + +
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Residues in contact with GLU 598 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594H SER* 3.1 18.2 + - - +
595H ARG* 3.1 34.1 - - - +
596H ILE 3.1 0.4 - - - -
597H VAL* 1.3 80.5 - - + +
599H TRP* 1.3 68.5 + - + +
601H GLU* 3.3 22.8 + - - +
602H ARG* 3.4 10.7 + - - +
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Residues in contact with TRP 599 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H LEU* 3.8 28.7 - - + +
372H MET* 3.6 46.9 - - + -
373H ASP* 3.2 33.6 + - - -
376H PHE* 3.9 20.9 - + + -
384H ILE* 5.0 4.3 - - + -
577H LEU* 4.9 0.4 - - + -
580H ILE* 4.1 20.6 - - + -
595H ARG* 3.6 20.6 - - + +
596H ILE 3.4 2.2 + - - +
597H VAL 3.3 0.2 - - - -
598H GLU* 1.3 79.3 + - + +
600H LYS* 1.3 57.2 + - - +
601H GLU 2.9 6.1 - - - -
602H ARG* 3.6 28.5 - - + -
603H LEU* 2.9 61.1 + - + +
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Residues in contact with LYS 600 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580H ILE* 2.7 35.8 + - + +
581H TRP 4.2 7.9 + - - -
582H TYR 4.6 1.2 + - - -
583H ARG 3.2 24.5 + - - -
584H PRO* 4.4 2.9 - - - +
585H VAL* 3.4 36.6 - - + +
596H ILE* 3.2 24.8 + - - +
597H VAL* 3.1 16.9 + - + +
599H TRP* 1.3 75.8 - - - +
601H GLU* 1.3 58.9 + - + +
603H LEU* 5.0 2.7 - - - -
604H ASP* 2.6 35.1 - - - +
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Residues in contact with GLU 601 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597H VAL* 3.1 29.8 - - + +
598H GLU* 3.5 16.6 - - - +
599H TRP 2.9 0.4 - - - -
600H LYS* 1.3 80.8 - - + +
602H ARG* 1.3 59.3 + - - +
603H LEU 3.4 0.4 - - - -
604H ASP* 4.0 2.7 - - - +
605H LYS* 3.0 30.4 + - - +
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Residues in contact with ARG 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376H PHE* 3.5 30.6 + - - +
384H ILE* 4.6 17.7 - - + +
598H GLU 3.4 9.6 + - - +
599H TRP* 3.2 40.6 + - + +
601H GLU* 1.3 77.7 - - - +
603H LEU* 1.3 66.4 + - + +
605H LYS* 3.2 13.7 + - - +
606H GLU* 3.0 56.1 + - + +
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Residues in contact with LEU 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H ILE* 4.9 8.3 - - + -
388H MET* 3.7 16.4 - - + -
577H LEU* 3.6 34.1 - - + +
580H ILE* 5.0 7.2 - - + -
581H TRP* 3.6 38.3 - - + +
599H TRP* 2.9 57.3 + - + +
600H LYS* 5.0 2.7 - - - -
602H ARG* 1.3 80.5 - - + +
604H ASP* 1.3 58.3 + - - +
606H GLU* 4.1 3.5 - - - +
607H PHE* 2.8 36.2 + - - +
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Residues in contact with ASP 604 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581H TRP* 5.1 9.3 - - - -
600H LYS* 2.6 30.1 + - - +
601H GLU* 3.7 4.8 + - - +
602H ARG 3.4 0.6 - - - -
603H LEU* 1.3 79.5 - - - +
605H LYS* 1.3 60.3 + - - +
607H PHE 3.3 19.0 - - - +
608H SER* 4.4 4.9 + - - -
609H LEU* 4.4 17.3 - - - +
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Residues in contact with LYS 605 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H GLU 3.0 20.6 + - - +
602H ARG* 3.3 15.9 - - - +
603H LEU 3.1 0.2 - - - -
604H ASP* 1.3 80.3 - - - +
606H GLU* 1.3 71.9 + - - +
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Residues in contact with GLU 606 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H ILE* 4.6 14.3 - - + +
602H ARG* 3.0 48.3 + - + +
603H LEU* 4.1 2.2 - - - +
605H LYS* 1.3 91.0 - - + +
607H PHE* 1.3 85.4 + - + +
608H SER 4.3 0.4 + - - -
611H VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 607 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H ILE* 4.1 13.7 - - + -
385H GLU* 3.4 51.8 - - + -
388H MET* 4.1 18.2 - - + -
581H TRP* 3.8 19.7 - - + -
603H LEU* 2.8 30.4 + - - +
604H ASP* 3.3 16.3 - - - +
606H GLU* 1.3 96.7 - - + +
608H SER* 1.3 65.5 + - - +
611H VAL* 3.5 34.3 - - + -
612H TYR* 5.1 1.8 - - + +
615H MET* 4.2 21.3 - - + -
626H LEU* 5.5 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
------------------------------------------------------------
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