Contacts of the helix formed by residues 685 - 695 (chain N) in PDB entry 5D4D
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 ASP 685 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187L GLY 6.2 0.2 - - - -
188L GLN* 3.2 41.1 + - + +
683N ILE 5.1 1.0 - - - +
684N LYS* 1.3 80.9 - - - +
686N GLU* 1.3 70.5 + - - +
687N VAL 3.3 0.2 - - - -
688N TRP* 3.3 21.4 + - - +
689N ASP* 3.3 18.4 - - - +
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Residues in contact with GLU 686 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664N LYS* 5.6 0.3 - - - +
666N ILE* 3.8 29.9 - - + +
684N LYS* 3.2 31.3 - - - +
685N ASP* 1.3 80.9 - - - +
687N VAL* 1.3 60.6 + - - +
689N ASP* 3.1 12.7 + - - +
690N ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 687 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650N LEU* 4.7 7.6 - - + -
657N LEU* 3.7 6.6 - - + +
661N MET* 4.1 20.4 - - + -
666N ILE* 3.9 23.6 - - + -
676N MET* 4.5 5.4 - - + -
677N LEU* 4.5 7.4 - - + -
683N ILE* 3.6 24.5 - - + -
684N LYS* 3.2 31.2 - - + +
686N GLU* 1.3 76.2 - - - +
688N TRP* 1.3 70.6 + - + +
690N ALA* 3.6 9.1 - - - +
691N LEU* 2.9 28.2 + - - +
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Residues in contact with TRP 688 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ARG* 5.6 3.8 - - - +
188L GLN* 3.8 26.9 - - - +
646N LYS* 3.7 57.8 - - + +
647N ARG* 4.2 29.6 - - - -
650N LEU* 4.2 19.3 - - + -
683N ILE* 3.6 24.1 + - + +
684N LYS 3.5 24.2 + - - -
685N ASP* 3.3 18.7 + - - +
686N GLU 3.1 0.8 - - - -
687N VAL* 1.3 78.5 - - + +
689N ASP* 1.3 65.0 + - - +
691N LEU* 3.2 28.1 + - + +
692N GLU* 2.9 32.1 + - + +
720N LEU* 4.9 2.0 - - + +
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Residues in contact with ASP 689 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ARG* 3.3 27.7 + - - +
187L GLY* 5.0 4.2 - - - +
664N LYS* 6.4 0.4 - - - -
685N ASP* 3.3 18.5 - - - +
686N GLU* 3.1 11.6 + - - +
688N TRP* 1.3 76.4 - - - +
690N ALA* 1.3 64.7 + - - +
692N GLU* 3.1 11.0 + - - +
693N GLU* 3.0 34.3 + - - +
51O LEU* 3.1 39.3 - - + +
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Residues in contact with ALA 690 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657N LEU* 3.9 9.9 - - + -
660N LYS* 3.7 21.6 - - + +
661N MET* 4.8 2.7 - - + -
664N LYS* 4.5 6.0 - - + +
666N ILE* 4.0 19.1 - - + -
686N GLU 2.9 16.6 + - - +
687N VAL* 3.6 7.9 - - - +
689N ASP* 1.3 77.2 - - - +
691N LEU* 1.3 54.8 + - - +
693N GLU* 3.1 12.5 + - - +
694N VAL* 2.9 29.5 + - - +
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Residues in contact with LEU 691 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646N LYS 4.0 5.8 - - - +
649N ALA* 4.1 15.3 - - + +
650N LEU* 3.7 31.9 - - + +
653N PHE* 4.4 3.1 - - + -
657N LEU* 3.6 19.5 - - + +
687N VAL 2.9 18.1 + - - +
688N TRP* 3.3 29.6 - - + +
690N ALA* 1.3 74.7 - - - +
692N GLU* 1.3 64.7 + - - +
694N VAL* 3.0 21.2 + - + +
695N ILE* 3.2 28.8 + - + +
720N LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 692 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ARG* 3.3 39.9 + - - +
688N TRP* 2.9 21.7 + - + +
689N ASP* 3.1 9.4 + - - +
691N LEU* 1.3 75.5 - - - +
693N GLU* 1.3 61.6 + - + +
695N ILE* 3.8 9.2 + - - +
696N HIS* 3.6 21.7 + - - +
720N LEU* 3.8 36.2 + - + +
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Residues in contact with GLU 693 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660N LYS* 4.3 22.4 + - - +
664N LYS* 3.2 38.9 + - - -
689N ASP* 3.0 20.8 + - - +
690N ALA* 3.1 8.7 + - - +
692N GLU* 1.3 76.7 - - + +
694N VAL* 1.3 63.9 + - - +
695N ILE 3.4 0.4 + - - -
696N HIS* 3.8 11.4 + - - +
48O MET* 4.3 23.5 - - - +
49O GLN 5.8 0.9 - - - +
50O THR* 3.8 33.5 - - + +
51O LEU* 4.9 3.3 + - - +
58O PRO* 4.3 12.6 - - - +
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Residues in contact with VAL 694 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653N PHE* 3.8 24.9 - - + -
656N PHE* 3.6 45.7 - - + +
657N LEU* 3.7 13.0 - - + +
660N LYS* 3.6 19.1 - - + +
690N ALA 2.9 16.1 + - - +
691N LEU* 3.0 12.8 + - + +
693N GLU* 1.3 79.9 - - - +
695N ILE* 1.3 65.8 + - + +
696N HIS 3.4 1.6 + - - +
698N LYS* 3.9 19.1 + - - +
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Residues in contact with ILE 695 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653N PHE* 3.7 37.2 - - + -
691N LEU* 3.4 21.5 - - + +
692N GLU* 3.9 14.6 - - - +
694N VAL* 1.3 82.8 - - + +
696N HIS* 1.3 69.8 + - - +
697N GLY 3.2 0.9 + - - -
698N LYS* 3.0 29.8 + - - +
718N PRO* 3.7 37.6 - - + +
720N LEU* 3.8 29.4 - - + +
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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