Contacts of the helix formed by residues 685 - 705 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700N PHE* 5.4 6.4 - - - -
703N MET* 4.8 5.4 - - - +
859N SER* 5.9 1.0 - - - -
683O VAL 3.8 3.0 + - - -
684O VAL* 1.3 77.0 - - - +
686O PRO* 1.3 70.6 - - + +
687O ARG* 2.9 32.7 + - + +
688O VAL* 3.3 25.6 - - - +
689O ALA* 3.5 14.6 + - - +
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Residues in contact with PRO 686 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684O VAL 4.4 1.8 - - - +
685O ASP* 1.3 85.3 - - + +
687O ARG* 1.3 59.0 + - + +
689O ALA* 3.9 2.0 - - + -
690O SER* 2.9 39.1 + - - +
449P GLN* 3.5 21.3 - - - +
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Residues in contact with ARG 687 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699N GLU* 4.6 4.4 - - + +
703N MET* 3.5 51.6 - - + +
685O ASP* 2.9 19.7 + - + +
686O PRO* 1.3 77.7 - - + +
688O VAL* 1.3 65.2 + - - +
690O SER* 3.8 3.0 - - - -
691O ALA* 2.9 26.4 + - - +
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Residues in contact with VAL 688 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696N ALA* 4.0 12.6 - - + +
699N GLU 3.5 22.0 - - - +
700N PHE* 3.5 30.1 - - + +
859N SER* 4.5 7.0 - - - +
860N THR* 5.8 0.2 - - - -
863N ALA* 3.5 13.4 - - + +
684O VAL* 3.7 22.2 - - + -
685O ASP* 3.3 29.2 - - - +
687O ARG* 1.3 73.8 - - + +
689O ALA* 1.3 60.7 + - - +
691O ALA* 3.8 5.1 - - - +
692O ALA* 2.9 32.6 + - - +
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Residues in contact with ALA 689 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863N ALA* 4.0 11.6 - - - +
866N LEU* 4.8 8.0 - - + +
867N ALA 5.9 0.2 + - - -
684O VAL* 4.4 10.3 - - + -
685O ASP 3.5 7.8 + - - +
686O PRO 3.9 2.5 - - - +
687O ARG 3.1 0.4 - - - -
688O VAL* 1.3 82.6 - - - +
690O SER* 1.3 57.2 + - - +
692O ALA* 3.9 1.2 - - - +
693O ALA* 2.9 30.4 + - - +
448P PRO* 5.8 3.8 - - + +
449P GLN* 3.5 35.2 - - + +
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Residues in contact with SER 690 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686O PRO* 2.9 23.5 + - - +
687O ARG* 4.0 2.7 - - - -
689O ALA* 1.3 77.3 - - - +
691O ALA* 1.3 57.9 + - - +
693O ALA* 3.6 6.0 - - - +
694O LYS* 2.9 32.8 + - - +
447P ASP* 5.3 9.8 - - - +
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Residues in contact with ALA 691 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695N SER* 2.7 20.8 + - - +
699N GLU* 3.5 35.2 - - + -
687O ARG 2.9 17.9 + - - +
688O VAL 3.8 2.9 - - - +
690O SER* 1.3 73.9 - - - +
692O ALA* 1.3 63.7 + - - +
694O LYS* 3.1 15.1 - - - +
695O SER 3.0 17.5 + - - -
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Residues in contact with ALA 692 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692N ALA* 3.4 23.8 - - - +
695N SER* 3.3 8.6 + - - -
696N ALA* 3.8 2.9 - - + +
863N ALA* 3.3 32.8 - - + +
867N ALA* 3.1 12.2 - - + +
688O VAL 2.9 18.1 + - - +
689O ALA 4.0 0.7 - - - +
691O ALA* 1.3 75.6 - - - +
693O ALA* 1.3 58.3 + - - +
696O ALA* 2.9 26.2 + - - +
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Residues in contact with ALA 693 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867N ALA* 3.6 15.2 - - + +
870N ALA* 5.0 0.2 - - + -
689O ALA 2.9 19.6 + - - +
690O SER* 3.6 7.0 - - - +
692O ALA* 1.3 77.4 - - - +
694O LYS* 1.3 64.5 + - - +
696O ALA* 3.8 0.3 - - - -
697O LEU* 2.9 38.7 + - + +
445P ALA 5.3 0.2 - - - +
446P ARG 4.8 9.4 - - - +
447P ASP* 5.6 0.7 - - - -
448P PRO* 4.6 21.8 - - + -
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Residues in contact with LYS 694 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695N SER* 4.4 4.2 + - - -
699N GLU* 6.2 1.1 - - - -
690O SER 2.9 19.2 + - - +
691O ALA* 3.1 25.1 - - - +
693O ALA* 1.3 73.2 - - - +
695O SER* 1.3 71.3 + - - +
697O LEU* 3.8 4.2 - - - +
698O GLU* 2.9 57.5 + - + +
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Residues in contact with SER 695 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691N ALA* 3.6 20.8 + - - +
695N SER* 3.4 20.7 - - - -
691O ALA 3.0 18.1 + - - -
692O ALA 4.0 1.1 - - - -
694O LYS* 1.3 92.9 + - - +
696O ALA* 1.3 58.7 + - - +
698O GLU* 3.3 5.3 + - - +
699O GLU* 2.9 32.1 + - - +
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Residues in contact with ALA 696 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688N VAL* 3.4 23.6 - - + +
691N ALA* 4.4 2.6 - - - +
692N ALA* 3.7 12.1 - - + +
867N ALA* 3.5 21.5 - - + +
868N ALA 4.8 0.2 - - - +
871N VAL* 3.5 14.8 - - + -
692O ALA 2.9 19.0 + - - +
693O ALA 3.8 0.7 - - - +
695O SER* 1.3 76.3 - - - +
697O LEU* 1.3 58.2 + - - +
699O GLU 3.5 0.3 + - - -
700O PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 697 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867N ALA 4.6 0.2 - - - +
870N ALA* 3.8 23.6 - - + -
871N VAL* 3.8 24.2 - - + -
874N LYS* 3.4 45.8 - - + +
693O ALA* 2.9 31.5 + - + +
694O LYS* 4.1 4.5 - - - +
696O ALA* 1.3 76.3 - - - +
698O GLU* 1.3 59.2 + - - +
700O PHE* 3.4 5.2 + - + +
701O SER* 2.9 27.5 + - - -
445P ALA* 4.2 18.4 - - + +
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Residues in contact with GLU 698 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694O LYS* 2.9 45.8 + - + +
695O SER* 3.8 5.2 - - - +
697O LEU* 1.3 76.5 - - + +
699O GLU* 1.3 59.8 + - + +
701O SER* 3.2 8.3 + - - -
702O LYS* 3.0 46.5 + - + +
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Residues in contact with GLU 699 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687N ARG* 3.1 36.8 + - - +
688N VAL* 4.1 11.9 - - + -
691N ALA* 3.5 29.4 - - + -
695O SER* 2.9 17.1 + - - +
696O ALA 4.0 2.7 - - - +
698O GLU* 1.3 73.5 - - + +
700O PHE* 1.3 61.2 + - - +
702O LYS* 3.3 18.4 + - - +
703O MET* 2.9 32.1 + - - +
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Residues in contact with PHE 700 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684N VAL* 5.7 3.4 - - + -
685N ASP* 5.4 0.7 - - - -
688N VAL* 3.9 16.3 - - + +
871N VAL* 4.0 33.4 - - + -
874N LYS* 4.2 17.3 - - + -
875N HIS* 4.1 22.0 - - + -
696O ALA 2.9 18.9 + - - +
697O LEU* 3.7 9.0 - - + +
698O GLU 3.3 0.2 - - - -
699O GLU* 1.3 72.6 - - - +
701O SER* 1.3 61.5 + - - +
703O MET* 3.2 3.6 + - + +
704O LYS* 2.9 47.7 + - - +
212Q VAL* 4.2 16.4 - - + -
214Q ASP* 4.0 11.4 - - - -
216Q ARG* 3.1 31.4 - - - -
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Residues in contact with SER 701 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697O LEU 2.9 15.7 + - - -
698O GLU* 3.3 12.6 - - - -
699O GLU 3.2 0.2 - - - -
700O PHE* 1.3 77.4 - - - +
702O LYS* 1.3 61.6 + - - +
704O LYS* 2.7 27.2 + - - +
705O GLU* 2.7 33.1 + - - +
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Residues in contact with LYS 702 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687N ARG* 5.2 2.4 + - - +
698O GLU* 3.0 37.5 + - - +
699O GLU* 3.3 23.8 + - - +
701O SER* 1.3 81.9 + - - +
703O MET* 1.3 60.5 + - - +
705O GLU* 3.1 34.0 - - - +
706O GLU* 4.7 1.7 - - - +
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Residues in contact with MET 703 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617N LYS* 5.9 2.9 - - + -
685N ASP* 3.4 26.0 - - - +
687N ARG* 2.7 46.9 - - - +
688N VAL* 4.1 12.1 - - + -
699O GLU 2.9 18.1 + - - +
700O PHE* 3.5 11.2 - - + +
701O SER 3.0 0.2 - - - -
702O LYS* 1.3 75.4 - - - +
704O LYS* 1.3 65.0 + - - +
705O GLU 3.1 2.5 - - - -
706O GLU* 3.1 55.0 - - - +
214Q ASP* 3.7 14.4 - - - +
216Q ARG* 3.2 10.1 + - - +
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Residues in contact with LYS 704 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874N LYS* 4.4 19.4 - - - +
875N HIS* 6.1 0.4 - - - +
878N ALA* 5.3 11.5 - - - +
882N ARG* 5.6 6.1 - - - +
700O PHE* 2.9 39.0 + - + +
701O SER* 2.7 28.8 + - - +
703O MET* 1.3 71.7 - - - +
705O GLU* 1.3 59.8 + - - +
706O GLU 4.1 0.3 + - - -
874O LYS* 4.7 4.0 + - - -
216Q ARG* 3.3 38.6 - - - +
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Residues in contact with GLU 705 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701O SER* 2.7 37.0 + - - +
702O LYS* 3.1 34.6 - - + +
703O MET 4.0 0.2 - - - -
704O LYS* 1.3 79.9 - - - +
706O GLU* 1.3 61.9 + - - +
874O LYS* 4.2 13.9 - - + +
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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
------------------------------------------------------------
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