Contacts of the helix formed by residues 701 - 711 (chain B) in PDB entry 1LDK
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 LYS 701 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697B GLU* 2.9 14.6 + - + +
700B HIS* 1.3 82.4 - - + +
702B ASN* 1.3 54.1 + - - +
703B ILE* 2.8 8.7 - - + -
704B GLU* 2.8 60.0 + - + +
705B GLU* 3.8 3.7 + - - +
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Residues in contact with ASN 702 (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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464B LYS* 2.5 62.7 + - - +
468B LYS* 4.6 9.0 - - - +
698B THR 3.1 24.3 + - - +
699B THR* 3.4 17.7 - - - +
701B LYS* 1.3 81.4 - - - +
703B ILE* 1.3 50.1 + - - +
704B GLU 3.2 0.2 - - - -
705B GLU* 2.9 39.3 + - - +
706B ASP* 4.7 0.5 - - - +
1106C TYR 4.0 18.1 + - - +
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Residues in contact with ILE 703 (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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460B ASP* 3.0 34.1 - - + +
461B VAL* 3.4 23.1 - - + -
464B LYS* 3.0 28.0 + - + +
465B PHE* 6.1 2.7 - - + -
699B THR 4.1 2.8 + - - +
700B HIS* 2.9 27.7 + - + +
701B LYS* 2.8 3.3 - - + +
702B ASN* 1.3 79.3 + - - +
704B GLU* 1.3 83.8 + - + +
706B ASP* 3.1 13.1 + - + +
707B ARG* 3.1 42.6 + - - +
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Residues in contact with GLU 704 (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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701B LYS* 2.8 40.6 + - + +
703B ILE* 1.3 87.4 - - + +
705B GLU* 1.3 67.1 + - + +
707B ARG* 3.0 26.3 + - - +
708B LYS* 3.0 47.7 + - + +
745B ARG* 4.5 16.3 + - - -
748B VAL* 4.8 5.9 - - - +
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Residues in contact with GLU 705 (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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464B LYS* 4.8 0.4 - - - +
701B LYS 4.5 2.5 - - - +
702B ASN* 2.9 36.3 + - - +
704B GLU* 1.3 77.4 - - + +
706B ASP* 1.3 61.8 + - - +
709B LEU* 2.8 45.9 + - + +
1069C THR* 5.5 1.6 + - - -
1081C PHE* 4.5 16.6 - - - -
1106C TYR 5.7 4.3 - - - +
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Residues in contact with ASP 706 (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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460B ASP* 5.8 1.8 - - - +
463B GLN* 5.6 3.8 - - - +
464B LYS* 3.2 34.7 + - - +
702B ASN 4.6 0.2 - - - +
703B ILE* 3.1 6.1 + - + +
705B GLU* 1.3 81.1 - - - +
707B ARG* 1.3 63.9 + - - +
708B LYS 3.2 2.6 + - - -
709B LEU* 4.3 3.9 - - - +
710B LEU* 2.9 45.0 + - + +
742B PHE* 4.6 3.4 - - + -
1103C PHE* 5.4 0.2 - - - -
1106C TYR* 2.8 49.7 - - - +
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Residues in contact with ARG 707 (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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416B SER* 4.5 7.1 + - - -
458B ASP* 3.5 17.0 + - - -
460B ASP* 3.0 20.4 + - - -
461B VAL* 3.5 11.1 - - - +
703B ILE* 3.1 41.9 + - - +
704B GLU* 3.0 23.8 + - - +
706B ASP* 1.3 70.8 - - - +
708B LYS* 1.3 77.6 + - + +
711B ILE* 2.8 36.8 - - + +
742B PHE* 2.8 60.3 - - + +
743B LYS 4.4 4.6 + - - +
744B PRO* 6.0 2.6 - - + +
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Residues in contact with LYS 708 (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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704B GLU* 3.0 52.6 + - + +
707B ARG* 1.3 88.2 - - + +
709B LEU* 1.3 72.7 + - + +
710B LEU 3.1 2.2 - - - -
711B ILE* 2.9 14.9 + - - +
712B GLN* 3.2 16.3 + - + +
744B PRO* 6.1 1.8 - - - +
748B VAL* 3.4 31.5 + - - +
751B LYS* 6.3 2.9 - - + +
752B CYS* 3.4 39.9 - - + -
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Residues in contact with LEU 709 (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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705B GLU* 2.8 40.9 + - + +
706B ASP* 4.5 5.2 - - - +
708B LYS* 1.3 81.2 - - + +
710B LEU* 1.3 60.5 + - - +
712B GLN* 3.2 24.1 + - + +
713B ALA* 5.0 2.1 - - - +
755B ILE* 6.5 0.2 - - + -
759B LYS* 5.4 7.2 - - - +
1067C GLU* 3.1 24.9 - - - +
1081C PHE* 3.0 37.2 - - + -
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Residues in contact with LEU 710 (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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706B ASP* 2.9 42.3 + - + +
707B ARG 4.5 1.3 - - - +
709B LEU* 1.3 77.2 - - - +
711B ILE* 1.3 59.5 + - + +
712B GLN 3.1 1.7 + - - -
713B ALA* 3.5 6.9 + - - +
714B ALA* 3.0 27.7 + - + +
717B ARG* 5.0 1.7 + - - -
738B LEU* 5.4 11.2 - - + -
741B ARG* 5.7 8.1 - - + -
742B PHE* 4.3 18.6 - - + -
1103C PHE* 4.9 9.4 - - + -
1106C TYR* 4.3 16.2 - - + +
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Residues in contact with ILE 711 (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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707B ARG 2.8 24.7 - - - +
708B LYS* 2.9 6.8 + - - +
710B LEU* 1.3 75.4 - - + +
712B GLN* 1.3 74.0 + - - +
713B ALA 3.0 5.6 - - - -
714B ALA* 3.4 11.4 - - + -
715B ILE* 2.7 34.4 - - + +
734B VAL* 4.0 17.9 - - + -
735B LEU* 6.5 0.7 - - + -
738B LEU* 4.6 8.3 - - + -
742B PHE* 4.3 21.3 - - + -
744B PRO* 5.2 6.7 - - + -
749B ILE* 6.1 4.0 - - + -
752B CYS* 4.9 9.2 - - - -
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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
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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