Contacts of the helix formed by residues 619 - 628 (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 ASN 619 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414G ALA 3.8 10.1 + - - -
415G LEU* 3.5 28.9 + - - +
418G PRO* 4.0 10.6 - - + +
431G GLN* 3.1 27.7 + - - +
439G ALA* 4.1 21.8 - - + +
443G LEU* 5.5 3.0 - - + +
617G PRO* 4.2 1.9 + - - +
618G LEU* 1.3 81.1 - - - +
620G ASP* 1.3 63.1 + - - +
621G ASN 4.2 1.8 - - - +
622G VAL* 4.1 19.6 - - + +
623G ALA* 3.1 22.6 + - - +
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Residues in contact with ASP 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP* 5.8 4.7 - - - +
419G ARG 5.7 2.5 - - - +
420G ILE* 6.5 1.3 - - + -
618G LEU* 3.4 11.7 + - - +
619G ASN* 1.3 70.9 - - - +
621G ASN* 1.3 60.7 + - - +
623G ALA* 3.6 7.8 - - - +
624G ALA* 2.8 29.1 + - - +
664G ARG* 4.9 6.2 - - - +
665G GLY* 4.3 13.5 + - - -
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Residues in contact with ASN 621 (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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414G ALA* 3.5 30.0 - - + +
417G THR 5.0 0.6 + - - -
418G PRO* 4.0 14.5 - - + +
419G ARG* 3.6 53.3 + - + +
619G ASN* 3.2 1.0 - - + -
620G ASP* 1.3 76.0 - - - +
622G VAL* 1.3 66.4 + - + +
624G ALA* 3.2 9.3 + - - +
625G LEU* 3.0 28.1 + - - +
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Residues in contact with VAL 622 (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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406G LEU* 4.9 4.3 - - + -
411G PHE* 4.0 21.1 - - + -
414G ALA* 3.7 33.9 - - + +
415G LEU* 3.9 14.6 - - + +
443G LEU* 3.4 34.3 - - + -
619G ASN* 3.6 16.6 + - + +
620G ASP 3.4 0.2 - - - -
621G ASN* 1.3 73.0 - - - +
623G ALA* 1.3 65.1 + - - +
625G LEU* 3.0 19.5 + - + +
626G LEU* 3.0 19.6 + - + +
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Residues in contact with ALA 623 (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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443G LEU* 4.9 2.8 - - - +
618G LEU* 5.0 11.0 - - + -
619G ASN 3.1 18.9 + - - +
620G ASP* 3.6 11.0 - - - +
622G VAL* 1.3 77.7 - - - +
624G ALA* 1.3 55.9 + - - +
626G LEU* 3.2 15.4 + - - +
627G HIS* 2.9 26.5 + - - +
638G TRP* 4.7 20.5 - - + +
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Residues in contact with ALA 624 (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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620G ASP 2.8 16.2 + - - +
621G ASN* 3.3 14.8 - - - +
623G ALA* 1.3 74.5 - - - +
625G LEU* 1.3 64.2 + - + +
627G HIS* 3.0 20.4 + - - +
628G GLN* 3.1 27.0 + - - +
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Residues in contact with LEU 625 (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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406G LEU* 3.6 26.3 - - + +
410G ASP* 3.8 25.1 - - + +
411G PHE* 3.9 15.0 - - + +
414G ALA* 3.5 31.2 - - + -
621G ASN* 3.0 21.1 + - - +
622G VAL* 3.0 13.5 + - + +
624G ALA* 1.3 79.0 - - + +
626G LEU* 1.3 62.7 + - - +
628G GLN* 3.0 31.6 + - - +
629G SER 3.2 8.5 + - - -
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Residues in contact with LEU 626 (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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375G PHE* 5.8 4.3 - - + -
404G LEU* 3.8 21.3 - - + -
406G LEU* 3.8 26.5 - - + -
443G LEU* 4.3 17.3 - - + -
447G THR* 4.7 3.1 - - - +
622G VAL* 3.0 17.8 + - + +
623G ALA* 3.2 8.3 + - - +
625G LEU* 1.3 76.4 - - - +
627G HIS* 1.3 57.2 + - - +
629G SER* 2.5 35.4 + - - +
634G THR* 4.6 3.8 - - - +
635G ALA* 3.6 9.7 - - - -
638G TRP* 3.2 55.2 - - + +
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Residues in contact with HIS 627 (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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623G ALA 2.9 13.3 + - - +
624G ALA* 3.0 15.9 + - - +
626G LEU* 1.3 76.0 - - - +
628G GLN* 1.3 61.3 + - + +
629G SER 3.4 1.0 + - - -
635G ALA* 4.3 14.2 + - - +
638G TRP* 3.2 31.6 + - - +
639G LYS* 4.1 24.6 - - + -
640G ASP 4.7 8.8 - - - -
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Residues in contact with GLN 628 (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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405G GLY 5.6 0.2 - - - +
624G ALA* 3.5 20.4 + - - +
625G LEU* 3.0 29.9 + - - +
627G HIS* 1.3 83.5 - - + +
629G SER* 1.3 68.9 + - - +
630G THR* 3.5 1.4 + - - -
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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