Contacts of the helix formed by residues 592 - 607 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362G THR* 4.1 11.7 - - + +
365G PHE* 3.6 33.2 - - + -
366G ASN* 3.4 31.9 - - - +
369G LEU* 4.5 4.0 - - + -
588G PHE* 3.6 13.5 - - + -
589G ALA* 3.0 40.9 + - + +
591G SER* 1.3 81.1 + - - +
593G GLN* 1.3 60.0 + - - +
594G SER 3.0 3.4 - - - -
595G ARG* 2.8 28.4 + - + +
596G ILE* 3.0 23.6 + - + +
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Residues in contact with GLN 593 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585G VAL* 3.1 44.6 - - + +
586G ALA* 4.3 8.5 + - - +
588G PHE* 3.6 9.4 + - + +
589G ALA 2.9 18.2 + - - +
590G GLN* 3.1 42.8 + - - +
591G SER 3.7 0.4 - - - -
592G ILE* 1.3 77.3 - - - +
594G SER* 1.3 59.3 + - - +
596G ILE* 4.0 4.0 - - - -
597G VAL* 3.1 30.3 + - - +
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Residues in contact with SER 594 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590G GLN 5.0 2.9 + - - -
591G SER 5.5 4.3 - - - -
592G ILE* 3.0 2.1 - - - +
593G GLN* 1.3 79.3 - - - +
595G ARG* 1.3 57.3 + - - +
597G VAL* 4.1 6.8 + - - +
598G GLU* 3.1 26.5 + - - +
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Residues in contact with ARG 595 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G ASN* 3.2 42.4 + - - +
369G LEU* 3.2 28.8 - - + +
370G ASP* 3.1 35.8 + - - +
373G ASP* 2.8 28.7 + - - -
592G ILE* 2.8 17.6 + - + +
594G SER* 1.3 79.0 - - - +
596G ILE* 1.3 65.1 + - - +
597G VAL 3.3 0.2 - - - -
598G GLU* 3.1 35.5 + - - +
599G TRP* 3.6 15.1 + - + +
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Residues in contact with ILE 596 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G PHE* 5.6 1.3 - - + -
369G LEU* 4.8 8.3 - - + -
576G LEU* 6.0 0.4 - - + -
580G ILE* 3.6 25.8 - - + +
585G VAL* 4.0 6.5 - - + -
588G PHE* 3.4 61.2 - - + -
592G ILE* 3.0 34.5 + - + +
593G GLN* 3.8 7.4 - - - +
594G SER 3.5 0.4 - - - -
595G ARG* 1.3 77.9 - - - +
597G VAL* 1.3 62.0 + - - +
598G GLU 3.3 0.2 + - - -
599G TRP 3.4 2.6 + - - -
600G LYS* 3.2 40.4 + - + +
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Residues in contact with VAL 597 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585G VAL* 3.7 22.9 - - + -
593G GLN 3.1 19.0 + - - +
594G SER* 4.3 7.0 - - - +
595G ARG 3.3 0.4 - - - -
596G ILE* 1.3 73.8 - - - +
598G GLU* 1.3 65.0 + - - +
600G LYS* 3.1 21.4 + - + +
601G GLU* 3.1 29.7 + - + +
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Residues in contact with GLU 598 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594G SER* 3.1 18.4 + - - +
595G ARG* 3.1 35.0 - - - +
596G ILE 3.1 0.4 - - - -
597G VAL* 1.3 80.5 - - - +
599G TRP* 1.3 68.1 + - + +
601G GLU* 3.3 22.3 + - - +
602G ARG* 3.4 11.1 + - - +
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Residues in contact with TRP 599 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G LEU* 3.8 28.1 - - + +
372G MET* 3.6 47.3 - - + -
373G ASP* 3.2 33.6 + - - -
376G PHE* 3.9 19.5 - + + -
384G ILE* 5.0 4.0 - - + -
577G LEU* 4.9 0.4 - - + -
580G ILE* 4.1 21.5 - - + -
595G ARG* 3.6 21.0 - - + +
596G ILE 3.4 2.7 + - - +
598G GLU* 1.3 79.0 + - + +
600G LYS* 1.3 57.8 + - - +
601G GLU 2.9 6.1 - - - -
602G ARG* 3.6 28.9 - - + -
603G LEU* 2.9 60.3 + - + +
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Residues in contact with LYS 600 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580G ILE* 2.7 35.7 + - + +
581G TRP 4.2 7.7 + - - -
582G TYR 4.6 1.2 + - - -
583G ARG 3.2 24.2 + - - -
584G PRO* 4.4 2.6 - - - +
585G VAL* 3.4 36.3 - - + +
596G ILE* 3.2 24.4 + - - +
597G VAL* 3.1 17.4 + - + +
599G TRP* 1.3 77.6 - - - +
601G GLU* 1.3 58.2 + - + +
603G LEU* 5.0 2.7 - - - -
604G ASP* 2.6 36.6 - - - +
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Residues in contact with GLU 601 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G VAL* 3.1 28.5 - - + +
598G GLU* 3.5 15.7 - - - +
599G TRP 2.9 0.2 - - - -
600G LYS* 1.3 82.1 - - + +
602G ARG* 1.3 60.0 + - - +
603G LEU 3.4 0.4 - - - -
604G ASP* 4.0 2.9 - - - +
605G LYS* 3.0 31.1 + - - +
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Residues in contact with ARG 602 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376G PHE* 3.5 31.4 + - - +
384G ILE* 4.6 17.3 - - + +
598G GLU 3.4 9.5 + - - +
599G TRP* 3.2 40.6 + - + +
601G GLU* 1.3 78.6 - - - +
603G LEU* 1.3 67.2 + - + +
605G LYS* 3.2 13.6 + - - +
606G GLU* 3.1 55.3 + - + +
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Residues in contact with LEU 603 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384G ILE* 4.9 9.2 - - + -
388G MET* 3.7 15.7 - - + -
577G LEU* 3.6 35.0 - - + +
580G ILE* 5.0 7.0 - - + -
581G TRP* 3.6 36.7 - - + +
599G TRP* 2.9 58.1 + - + +
600G LYS* 5.0 3.1 - - - -
602G ARG* 1.3 80.3 - - + +
604G ASP* 1.3 57.2 + - - +
606G GLU* 4.0 3.4 - - - +
607G PHE* 2.8 35.9 + - - +
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Residues in contact with ASP 604 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581G TRP* 5.1 9.3 - - - -
600G LYS* 2.6 29.7 + - - +
601G GLU* 3.7 3.1 + - - +
602G ARG 3.4 0.4 - - - -
603G LEU* 1.3 79.7 - - - +
605G LYS* 1.3 61.3 + - - +
607G PHE 3.3 18.6 - - - +
608G SER* 4.4 4.9 + - - -
609G LEU* 4.4 18.2 - - - +
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Residues in contact with LYS 605 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601G GLU 3.0 20.4 + - - +
602G ARG* 3.3 15.0 - - - +
603G LEU 3.1 0.2 - - - -
604G ASP* 1.3 80.9 - - - +
606G GLU* 1.3 72.3 + - - +
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Residues in contact with GLU 606 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384G ILE* 4.6 13.8 - - + +
602G ARG* 3.1 50.1 + - + +
603G LEU* 4.1 2.2 - - - +
605G LYS* 1.3 92.7 - - + +
607G PHE* 1.3 85.1 + - + +
608G SER 4.3 0.2 - - - -
611G VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 607 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384G ILE* 4.1 13.7 - - + -
385G GLU* 3.4 52.9 - - + -
388G MET* 4.2 17.5 - - + -
581G TRP* 3.8 20.7 - - + -
603G LEU* 2.8 27.3 + - - +
604G ASP* 3.3 15.7 - - - +
605G LYS 5.0 0.2 - - - -
606G GLU* 1.3 99.0 - - + +
608G SER* 1.3 65.4 + - - +
611G VAL* 3.5 32.3 - - + -
612G TYR* 5.1 1.3 - - + +
615G MET* 4.2 21.1 - - + -
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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