Contacts of the helix formed by residues 604 - 611 (chain B) in PDB entry 4DN5
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 604 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A PRO* 6.4 0.7 - - + -
560B GLU* 3.5 20.2 + - + +
561B THR* 3.7 35.0 - - + +
596B TRP* 3.8 24.5 - - + +
597B THR* 4.4 8.3 - - + -
600B PHE* 3.7 40.4 - - + +
601B ARG 4.7 0.2 - - - -
602B GLY* 4.1 12.3 - - - -
603B PRO* 1.3 71.4 - - - +
605B CYS* 1.3 64.1 + - - +
606B LEU 3.2 2.7 - - - -
607B LYS* 2.9 18.3 + - + -
608B ILE* 3.1 28.6 + - + +
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Residues in contact with CYS 605 (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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370A PRO* 6.3 1.3 - - - -
560B GLU* 3.3 31.6 - - - +
563B MET* 4.6 12.6 - - - -
568B VAL* 3.0 37.2 - - + +
603B PRO* 3.4 9.3 - - + -
604B LEU* 1.3 78.2 - - - +
606B LEU* 1.3 61.5 + - - +
608B ILE* 3.7 12.1 + - - +
609B ALA* 3.8 1.9 + - - +
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Residues in contact with LEU 606 (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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603B PRO* 4.4 4.1 + - + +
604B LEU 3.2 0.6 - - - -
605B CYS* 1.3 79.1 - - - +
607B LYS* 1.3 80.2 + - + +
609B ALA* 3.4 8.3 + - + +
610B SER* 3.2 41.9 + - - +
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Residues in contact with LYS 607 (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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596B TRP* 3.8 5.3 - - + -
600B PHE* 3.6 58.1 - - + -
601B ARG 5.7 0.7 - - - +
602B GLY 5.3 7.9 + - - +
603B PRO* 3.7 23.7 + - - +
604B LEU* 2.9 12.2 + - + +
606B LEU* 1.3 92.9 - - + +
608B ILE* 1.3 59.6 + - - +
610B SER* 4.6 2.7 - - - +
611B GLU* 2.9 40.0 + - + +
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Residues in contact with ILE 608 (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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560B GLU 3.4 25.1 - - - +
563B MET* 3.7 30.7 - - + +
565B PRO* 3.9 28.4 - - + +
568B VAL* 4.2 9.0 - - + -
580B TRP* 4.5 0.8 - - + -
596B TRP* 3.7 43.5 - - + +
604B LEU* 3.1 25.0 + - + +
605B CYS* 4.1 6.3 - - - +
606B LEU 3.4 0.2 - - - -
607B LYS* 1.3 76.2 - - - +
609B ALA* 1.3 61.6 + - - +
610B SER 3.5 0.5 + - - -
611B GLU 4.0 2.8 - - - +
636B LYS* 3.6 18.2 + - - -
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Residues in contact with ALA 609 (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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565B PRO* 5.0 5.2 - - - -
568B VAL* 4.3 9.1 - - + +
569B LEU* 3.8 36.1 - - + +
605B CYS 3.8 8.5 + - - +
606B LEU* 3.4 13.8 + - + +
607B LYS 3.3 0.4 - - - -
608B ILE* 1.3 81.3 - - - +
610B SER* 1.3 59.5 + - - +
636B LYS* 3.2 15.3 + - - +
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Residues in contact with SER 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 LEU* 3.2 33.2 + - - +
607B LYS* 4.4 2.5 - - - -
608B ILE 3.3 0.2 - - - -
609B ALA* 1.3 81.8 - - - +
611B GLU* 1.3 71.4 + - - +
612B PRO* 4.0 1.7 - - - +
636B LYS* 4.0 2.8 + - - -
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Residues in contact with GLU 611 (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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596B TRP* 3.7 15.0 - - + -
600B PHE* 3.5 37.4 - - + -
607B LYS* 2.9 25.1 + - + +
608B ILE 4.0 3.3 - - - +
610B SER* 1.3 80.6 - - - +
612B PRO* 1.4 77.9 - - + +
616B ARG* 5.2 5.9 + - - -
636B LYS* 2.7 30.9 + - - -
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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