Contacts of the helix formed by residues 685 - 702 (chain N) in PDB entry 6LTJ
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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617N LYS* 6.0 2.4 - - + +
618N ASP* 5.7 4.5 - - - +
684N VAL* 1.3 84.5 - - - +
686N PRO* 1.3 72.5 - - + +
687N ARG* 3.3 7.0 - - + +
688N VAL* 3.4 17.3 + - + +
689N ALA* 3.2 17.5 + - - +
700O PHE* 5.4 1.0 - - - -
703O MET* 3.4 25.1 - - + +
212Q VAL* 5.4 2.4 + - - +
214Q ASP* 3.1 44.5 - - - +
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Residues in contact with PRO 686 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613N LEU* 4.4 6.7 - - + -
617N LYS* 3.1 50.9 - - + +
618N ASP* 5.3 1.3 - - - +
620N TRP* 3.9 25.1 - - + +
639N PHE* 4.0 23.6 - - + -
684N VAL 4.1 1.8 - - - +
685N ASP* 1.3 85.1 - - + +
687N ARG* 1.3 60.5 + - + +
689N ALA* 3.8 6.7 - - + +
690N SER* 2.9 32.2 + - - -
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Residues in contact with ARG 687 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617N LYS* 4.2 31.7 - - + +
685N ASP* 3.3 3.5 - - + -
686N PRO* 1.3 77.3 - - + +
688N VAL* 1.3 57.6 + - + +
690N SER* 3.5 5.0 + - - -
691N ALA* 2.9 28.9 + - - +
699O GLU* 3.1 31.8 + - - +
702O LYS* 5.2 2.8 + - - +
703O MET* 2.7 49.6 - - - +
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Residues in contact with VAL 688 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684N VAL* 3.6 29.6 - - + -
685N ASP* 3.4 19.9 + - + +
686N PRO 3.3 0.4 - - - -
687N ARG* 1.3 73.7 - - - +
689N ALA* 1.3 62.1 + - - +
691N ALA* 3.4 7.6 + - - +
692N ALA* 3.0 27.5 + - - +
868N ALA* 5.7 0.9 - - - -
871N VAL* 4.1 8.5 - - + -
696O ALA* 3.4 32.0 - - + +
699O GLU* 4.1 4.9 - - - -
700O PHE* 3.9 27.6 - - + +
703O MET* 4.1 8.7 - - + -
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Residues in contact with ALA 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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620N TRP* 5.5 0.4 - - + -
640N LEU* 3.8 32.0 - - + +
681N ALA* 3.9 20.2 - - + +
684N VAL* 4.2 7.3 - - + +
685N ASP 3.2 16.1 + - - +
686N PRO* 3.8 7.0 - - + +
687N ARG 3.4 0.2 - - - -
688N VAL* 1.3 76.8 - - - +
690N SER* 1.3 56.3 + - - +
692N ALA* 3.3 5.8 + - - +
693N ALA* 2.9 30.7 + - - +
864N ALA* 4.7 1.8 - - - +
868N ALA* 5.9 2.5 - - + -
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Residues in contact with SER 690 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639N PHE* 3.6 30.0 + - - -
640N LEU* 4.7 6.0 + - - +
686N PRO 2.9 19.0 + - - -
687N ARG* 3.8 5.6 - - - -
689N ALA* 1.3 72.7 - - - +
691N ALA* 1.3 67.0 + - - +
693N ALA* 4.4 4.9 - - - -
694N LYS* 2.9 50.6 + - - +
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Residues in contact with ALA 691 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687N ARG 2.9 18.9 + - - +
688N VAL* 3.4 6.5 - - - +
690N SER* 1.3 76.0 - - - +
692N ALA* 1.3 62.8 + - - +
694N LYS* 4.2 3.7 - - - +
695N SER* 2.9 27.9 + - - -
695O SER* 3.6 18.8 + - - +
699O GLU* 3.5 31.2 - - + -
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Residues in contact with ALA 692 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688N VAL 3.0 16.5 + - - +
689N ALA* 3.8 5.2 - - - +
691N ALA* 1.3 75.4 - - - +
693N ALA* 1.3 64.1 + - - +
696N ALA* 3.0 26.7 + - - +
864N ALA* 3.8 17.7 - - - +
867N ALA* 3.6 30.3 - - + -
868N ALA* 5.0 1.1 - - - +
692O ALA* 3.4 15.1 - - + +
696O ALA* 3.7 5.3 - - + +
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Residues in contact with ALA 693 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640N LEU* 4.3 31.2 - - + +
641N ARG* 5.9 0.9 - - + -
689N ALA 2.9 17.7 + - - +
690N SER* 3.9 4.0 - - - +
692N ALA* 1.3 79.2 - - - +
694N LYS* 1.3 58.6 + - + +
696N ALA* 3.3 2.3 + - - +
697N LEU* 2.9 29.7 + - - +
860N THR* 4.5 8.5 - - - +
864N ALA* 3.8 17.9 - - + +
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Residues in contact with LYS 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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640N LEU 5.4 6.5 - - - +
690N SER* 2.9 41.8 + - - +
691N ALA* 4.2 3.1 - - - +
693N ALA* 1.3 70.8 - - + +
695N SER* 1.3 65.2 + - - +
697N LEU* 3.1 7.9 + - + +
698N GLU* 2.6 45.3 + - - +
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Residues in contact with SER 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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691N ALA 2.9 20.0 + - - -
692N ALA 3.6 3.8 - - - -
694N LYS* 1.3 77.2 - - - +
696N ALA* 1.3 56.2 - - - +
698N GLU* 3.4 5.0 + - - +
699N GLU* 2.9 34.1 + - - +
691O ALA* 2.7 32.6 + - - +
692O ALA* 4.0 1.3 - - - -
694O LYS* 4.4 4.2 + - - -
695O SER* 3.4 19.4 - - - -
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Residues in contact with ALA 696 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692N ALA 3.0 18.9 + - - +
693N ALA 3.8 3.6 - - - +
695N SER* 1.3 76.4 + - - +
697N LEU* 1.3 58.6 + - - +
699N GLU* 3.6 1.0 - - - +
700N PHE* 2.9 32.1 + - - +
860N THR* 3.9 16.6 - - - +
863N ALA* 3.6 31.4 - - + -
688O VAL* 4.0 16.7 - - + +
692O ALA* 3.8 4.0 - - + +
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Residues in contact with LEU 697 (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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641N ARG* 6.1 7.6 - - + -
693N ALA 2.9 18.1 + - - +
694N LYS* 3.1 8.3 + - - +
696N ALA* 1.3 76.8 - - - +
698N GLU* 1.3 81.0 + - + +
700N PHE* 3.3 3.7 + - + +
701N SER* 3.0 28.5 + - - +
860N THR* 3.6 25.3 - - + +
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Residues in contact with GLU 698 (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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694N LYS* 2.6 44.8 + - - +
695N SER* 4.0 5.2 + - - +
697N LEU* 1.3 89.3 - - + +
699N GLU* 1.3 68.8 + - - +
700N PHE 3.0 0.9 + - - -
701N SER* 3.1 9.3 + - - +
702N LYS* 2.8 39.9 + - + +
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Residues in contact with GLU 699 (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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695N SER* 2.9 18.9 + - - +
696N ALA 3.6 2.2 - - - +
698N GLU* 1.3 78.9 - - - +
700N PHE* 1.3 56.6 + - - +
702N LYS* 3.2 43.7 + - - +
703N MET* 3.2 27.2 - - - +
687O ARG* 4.6 4.1 - - + +
688O VAL* 3.5 14.8 + - - +
691O ALA* 3.5 30.7 - - + -
694O LYS* 6.2 1.3 - - - -
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Residues in contact with PHE 700 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696N ALA 2.9 16.8 + - - +
697N LEU* 3.7 3.4 - - + +
699N GLU* 1.3 76.8 - - - +
701N SER* 1.3 65.6 - - - +
702N LYS 3.0 9.3 + - - -
703N MET* 3.3 21.0 + - + +
859N SER* 4.0 24.7 - - - -
860N THR* 4.3 15.0 - - + -
685O ASP* 5.4 6.1 - - - -
688O VAL* 3.5 17.5 - - + -
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Residues in contact with SER 701 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697N LEU* 3.0 21.6 + - - +
698N GLU* 3.4 12.5 + - - +
700N PHE* 1.3 82.5 - - - +
702N LYS* 1.3 61.2 + - - +
703N MET 3.1 10.9 + - - +
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Residues in contact with LYS 702 (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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698N GLU* 2.8 23.9 + - + +
699N GLU* 3.2 34.7 + - - +
700N PHE 3.0 1.2 - - - -
701N SER* 1.3 78.6 - - - +
703N MET* 1.3 77.3 + - - +
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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