Contacts of the helix formed by residues 534 - 543 (chain G) in PDB entry 5JLH
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 LEU 534 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500G GLU* 3.2 30.1 - - - +
503G GLN* 3.6 7.6 - - + -
504G GLN* 3.2 38.4 - - + +
507G ASN* 3.5 17.3 - - - +
531G GLY 3.2 5.6 + - - +
532G LEU 3.2 0.6 - - - -
533G ASP* 1.3 79.0 - - + +
535G GLN* 1.3 64.6 + - - +
536G PRO 3.3 0.7 - - - -
537G CYS* 3.0 5.8 + - - -
538G ILE* 2.9 30.8 + - + +
599G TYR* 3.7 28.0 - - + +
723G GLU* 3.7 17.9 - - - +
726G ARG* 5.0 2.5 - - - +
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Residues in contact with GLN 535 (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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504G GLN* 3.2 23.0 + - - +
531G GLY 3.5 3.7 + - - +
532G LEU* 3.1 33.2 + - + +
534G LEU* 1.3 78.3 - - - +
536G PRO* 1.3 62.7 - - + +
538G ILE* 3.2 13.5 + - - +
539G ASP* 2.8 61.2 + - - +
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Residues in contact with PRO 536 (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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532G LEU 3.0 25.4 - - - +
533G ASP* 3.4 11.7 - - - +
535G GLN* 1.3 81.7 - - + +
537G CYS* 1.3 57.1 + - - +
539G ASP* 3.3 8.8 + - + +
540G LEU 2.9 23.7 + - - -
579G HIS* 2.9 28.1 + - + +
580G PRO* 5.8 4.0 - - + -
581G LYS* 4.8 11.4 - - + -
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Residues in contact with CYS 537 (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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500G GLU* 3.3 24.9 - - - +
534G LEU* 3.0 5.0 + - - +
536G PRO* 1.3 81.0 - - - +
538G ILE* 1.3 62.2 + - - +
540G LEU* 3.1 23.5 - - - +
541G ILE* 3.1 15.0 + - - +
579G HIS* 4.2 0.6 - - - -
581G LYS* 4.3 22.6 - - + +
596G VAL* 5.1 4.5 - - - -
597G LEU 4.0 16.6 - - - +
598G HIS* 3.7 30.1 - - - -
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Residues in contact with ILE 538 (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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497G TYR* 3.7 30.1 - - + +
500G GLU* 3.1 32.3 - - + -
501G LYS* 4.3 16.4 - - + -
504G GLN* 3.7 34.8 - - + +
534G LEU* 2.9 22.2 + - + +
535G GLN* 3.2 15.5 + - - +
537G CYS* 1.3 76.3 - - - +
539G ASP* 1.3 57.2 + - - +
541G ILE* 3.1 3.7 + - - +
542G GLU* 2.6 38.7 + - + +
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Residues in contact with ASP 539 (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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535G GLN* 2.8 53.3 + - - +
536G PRO* 3.7 7.7 - - + +
538G ILE* 1.3 73.5 - - - +
540G LEU* 1.3 68.3 + - - +
542G GLU* 3.8 12.0 - - - +
543G ARG* 2.9 54.0 + - + +
549G GLY* 4.2 2.1 - - - -
576G GLN* 4.7 2.6 + - - -
579G HIS* 5.4 1.8 - - + +
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Residues in contact with LEU 540 (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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536G PRO 2.9 14.3 + - - +
537G CYS* 3.1 12.6 - - - +
538G ILE 3.1 0.2 - - - -
539G ASP* 1.3 78.8 - - - +
541G ILE* 1.3 59.6 + - + +
549G GLY* 3.3 4.3 - - - -
550G LEU* 3.0 33.2 + - + +
576G GLN* 3.3 47.0 - - + +
579G HIS* 3.7 26.4 + - + +
581G LYS* 4.2 6.1 - - + -
582G PHE* 4.0 20.9 - - + +
596G VAL* 3.4 35.7 - - + -
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Residues in contact with ILE 541 (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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493G LEU* 3.9 30.3 - - + -
497G TYR* 3.8 35.7 - - + -
500G GLU* 5.7 2.0 - - + -
537G CYS* 3.1 17.0 + - - +
538G ILE* 3.1 6.5 + - - +
540G LEU* 1.3 80.1 - - + +
542G GLU* 1.3 59.3 + - - +
550G LEU* 3.3 23.0 + - + -
551G LEU* 3.1 49.1 + - + +
596G VAL* 5.5 2.9 - - + -
598G HIS* 4.0 22.4 - - + -
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Residues in contact with GLU 542 (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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2D GLU* 3.4 10.6 - - - +
497G TYR* 3.2 29.8 - - + +
501G LYS* 5.6 0.7 - - - -
538G ILE* 2.6 23.5 + - + +
539G ASP* 3.7 14.4 - - - +
541G ILE* 1.3 77.0 - - - +
543G ARG* 1.3 93.6 + - - +
544G PRO* 3.1 17.5 - - - +
549G GLY* 4.3 2.2 - - - -
551G LEU* 5.3 4.8 - - - +
552G ALA* 4.5 6.8 + - - +
675G LYS* 2.8 40.6 + - + +
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Residues in contact with ARG 543 (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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539G ASP* 2.9 42.4 + - + +
542G GLU* 1.3 81.6 + - - +
544G PRO* 1.3 68.9 - - + +
545G ALA* 3.7 11.9 - - - +
546G ASN* 2.2 50.6 + - - +
547G PRO* 3.3 19.5 - - - +
548G PRO 3.2 1.0 - - - -
549G GLY 2.5 34.1 + - - +
576G GLN* 6.1 1.6 - - - +
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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