Contacts of the helix formed by residues 680 - 695 (chain D) in PDB entry 1K0Y
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 ASN 680 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677D HIS* 2.9 12.5 + - + +
679D ASP* 1.4 83.1 + - + +
681D LEU* 1.4 59.0 + - - +
682D LYS* 3.3 5.6 + - - +
683D GLY* 3.3 26.2 + - - -
684D THR* 2.8 31.6 + - - +
1300D SO4 3.5 4.2 + - - -
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Residues in contact with LEU 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D VAL* 4.3 12.8 - - + -
674D GLY* 3.3 32.8 - - - +
677D HIS 3.7 5.4 - - - +
678D LEU* 4.0 20.6 - - + +
680D ASN* 1.4 74.3 - - - +
682D LYS* 1.4 55.0 + - - +
684D THR* 3.2 3.6 + - - -
685D PHE* 2.9 47.7 + - + -
733D VAL 4.6 1.8 - - - +
736D GLY* 3.6 29.6 - - - +
737D VAL* 3.9 11.7 - - + +
740D ALA* 3.5 17.0 - - + +
1300D SO4 2.6 25.0 + - - +
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Residues in contact with LYS 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D ASN* 4.9 2.0 - - - +
681D LEU* 1.4 76.0 - - - +
683D GLY* 1.4 62.0 + - - +
685D PHE 3.6 0.7 + - - -
686D ALA* 3.2 24.9 + - - +
739D ASN* 4.0 29.1 + - - +
740D ALA* 4.0 18.7 - - + +
743D HIS* 4.0 42.6 + - + +
1300D SO4 3.0 28.4 + - - +
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Residues in contact with GLY 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D ASN* 3.3 22.7 + - - -
682D LYS* 1.4 75.8 - - - +
684D THR* 1.4 62.5 + - - +
686D ALA* 3.7 14.8 + - - +
687D THR 5.3 0.3 + - - -
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Residues in contact with THR 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D ASP* 4.6 7.0 - - + +
674D GLY* 4.3 14.1 - - - +
677D HIS* 3.2 31.8 - - + +
680D ASN* 2.8 22.6 + - - +
681D LEU* 3.2 8.0 + - - -
683D GLY* 1.4 77.8 - - - +
685D PHE* 1.4 79.0 + - + +
686D ALA 3.9 0.3 + - - -
687D THR* 5.2 1.9 + - - -
688D LEU* 5.7 2.1 - - - +
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Residues in contact with PHE 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670D ALA* 3.5 28.9 - - + -
671D PHE* 4.4 6.1 - - - -
674D GLY* 3.8 25.4 - - - -
681D LEU* 2.9 39.2 + - + +
682D LYS 3.9 1.3 - - - -
684D THR* 1.4 81.2 - - + +
686D ALA* 1.4 52.7 + - - +
687D THR 3.4 2.2 - - - -
688D LEU* 3.2 27.0 + - + -
689D SER* 2.7 36.7 + - - -
737D VAL* 4.3 18.2 - - + -
740D ALA* 4.1 22.9 - - + -
741D LEU* 4.2 20.4 - - + -
748D HEM 4.1 16.8 - - + -
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Residues in contact with ALA 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682D LYS 3.2 16.8 + - - +
683D GLY* 3.7 12.1 + - - +
684D THR 3.6 2.2 - - - -
685D PHE* 1.4 74.7 - - - +
687D THR* 1.4 62.9 + - - +
689D SER* 3.3 7.9 + - - -
690D GLU* 3.1 32.1 + - - +
740D ALA 5.5 0.7 - - - -
743D HIS* 6.2 1.1 - - - +
744D LYS* 3.7 21.4 - - - +
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Residues in contact with THR 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683D GLY 5.3 0.2 + - - -
684D THR 5.2 1.9 + - - -
685D PHE 3.4 0.8 - - - -
686D ALA* 1.4 76.5 - - - +
688D LEU* 1.4 61.8 + - + +
690D GLU* 3.3 15.5 + - - +
691D LEU* 3.0 28.0 + - + +
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Residues in contact with LEU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670D ALA* 4.0 12.8 - - + -
684D THR 5.7 2.0 + - - +
685D PHE* 3.2 30.7 + - + +
687D THR* 1.4 82.5 - - + +
689D SER* 1.4 55.5 + - - +
691D LEU* 3.3 23.3 + - + +
692D HIS* 2.7 42.1 + - + +
741D LEU* 3.9 11.9 - - + -
748D HEM 4.0 41.5 - - + -
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Residues in contact with SER 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D PHE 2.7 20.3 + - - -
686D ALA* 3.4 7.9 - - - -
687D THR 3.2 0.2 - - - -
688D LEU* 1.4 72.7 - - - +
690D GLU* 1.4 62.3 + - - +
692D HIS* 3.3 1.2 + - - -
693D CYS* 3.0 23.6 + - - +
740D ALA 3.9 7.2 - - - -
741D LEU* 2.8 33.6 + - - +
742D ALA 3.9 0.3 - - - -
744D LYS* 2.8 36.4 + - - +
745D TYR* 3.7 5.0 - - - -
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Residues in contact with GLU 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D ALA* 3.1 25.4 + - - +
687D THR* 3.3 12.8 + - - +
689D SER* 1.4 73.6 - - - +
691D LEU* 1.4 55.9 + - - +
693D CYS* 4.6 3.6 - - - -
694D ASP* 2.8 51.0 + - - +
744D LYS* 3.9 29.8 - - + +
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Residues in contact with LEU 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687D THR* 3.0 14.9 + - + +
688D LEU* 3.3 24.0 + - + +
690D GLU* 1.4 74.7 - - - +
692D HIS* 1.4 60.1 + - + +
694D ASP* 5.5 0.2 - - - -
695D LYS* 2.9 56.9 + - + +
696D LEU* 3.0 30.0 + - + -
748D HEM 4.2 27.1 - - + +
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Residues in contact with HIS 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D LEU* 2.7 40.3 + - + +
689D SER* 3.8 3.8 - - - +
691D LEU* 1.4 77.3 - - + +
693D CYS* 1.4 55.6 + - - +
696D LEU* 3.6 15.3 - - + +
697D HIS 2.9 23.2 + - - -
698D VAL* 3.0 18.9 + - + -
703D PHE* 3.9 20.6 - + + -
741D LEU* 4.3 4.2 - - + +
745D TYR* 3.3 17.7 - - + +
748D HEM 2.1 84.0 + + + -
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Residues in contact with CYS 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 5.0 5.5 - - - +
689D SER 3.0 16.6 + - - +
690D GLU* 3.2 2.7 + - - +
692D HIS* 1.4 76.0 - - - +
694D ASP* 1.4 76.9 + - - +
697D HIS* 3.4 25.3 + - - +
744D LYS 4.5 3.6 - - - +
745D TYR* 3.6 51.1 + - + -
746D HIS* 4.0 18.4 - - - -
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Residues in contact with ASP 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690D GLU* 2.8 34.0 + - - +
691D LEU* 5.5 0.2 - - - -
693D CYS* 1.4 78.5 - - - +
695D LYS* 1.4 64.3 + - + +
697D HIS* 3.1 19.1 + - - -
746D HIS* 2.8 35.9 + - - -
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Residues in contact with LYS 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691D LEU* 2.9 37.9 + - + +
694D ASP* 1.4 80.9 - - + +
696D LEU* 1.4 70.1 + - + +
697D HIS* 3.6 14.5 + - - -
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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