Contacts of the helix formed by residues 682 - 703 (chain D) in PDB entry 1P93
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 SER 682 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586D ASN 4.8 1.4 + - - -
587D LEU* 4.1 11.6 - - - +
588D HIS* 3.4 24.7 + - - +
591D ASP* 2.8 15.1 + - - -
680D LEU* 2.7 4.8 + - - -
681D LYS* 1.3 75.2 + - - +
683D GLN* 1.3 60.8 + - - +
684D GLU* 2.7 20.9 + - - -
685D LEU* 3.0 13.9 + - - +
686D PHE* 3.0 20.8 + - - +
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Residues in contact with GLN 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675D VAL* 4.7 10.7 - - - +
679D GLY* 2.7 33.9 - - - -
680D LEU* 2.5 28.4 + - - +
681D LYS 3.5 0.8 - - - -
682D SER* 1.3 66.1 - - - +
684D GLU* 1.3 69.7 + - + +
686D PHE* 2.8 38.4 - - - +
687D ASP* 2.9 25.5 + - - +
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Residues in contact with GLU 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681D LYS 3.8 4.5 - - - +
682D SER* 2.7 30.7 + - - -
683D GLN* 1.3 77.9 + - + +
685D LEU* 1.3 97.8 + - - +
687D ASP* 3.0 7.1 + - - +
688D GLU* 2.9 21.6 + - - +
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Residues in contact with LEU 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D GLY* 4.0 5.2 - - - +
586D ASN* 3.7 32.1 - - + +
587D LEU* 3.5 15.0 - - + -
682D SER* 3.3 12.6 - - - +
684D GLU* 1.3 97.1 + - - +
686D PHE* 1.3 65.7 + - - +
688D GLU* 2.9 13.4 + - + +
689D ILE* 2.7 62.8 + - + +
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Residues in contact with PHE 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D LEU* 3.7 13.3 - - + +
595D LEU* 4.2 25.4 - - + -
672D LEU* 3.8 28.2 - - + +
675D VAL* 3.2 33.7 - - + -
680D LEU* 3.8 19.7 - - + -
682D SER 3.0 11.3 + - - +
683D GLN* 2.8 33.4 - - - +
685D LEU* 1.3 75.8 - - - +
687D ASP* 1.3 83.4 + - - +
689D ILE* 3.3 4.1 + - - +
690D ARG* 2.9 30.5 + - - +
772D LEU* 3.8 19.1 - - + -
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Residues in contact with ASP 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D GLN* 2.9 32.1 - - - +
684D GLU* 3.0 8.9 + - - +
686D PHE* 1.3 90.0 - - - +
688D GLU* 1.3 70.2 + - - +
690D ARG* 2.8 11.6 + - - +
691D MET* 2.6 27.5 + - - +
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Residues in contact with GLU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C LEU* 5.6 3.8 - - - +
684D GLU 2.9 12.6 + - - +
685D LEU* 2.9 21.0 + - + +
687D ASP* 1.3 75.2 - - - +
689D ILE* 1.3 60.9 + - + +
691D MET* 3.0 27.7 - - - +
692D THR* 3.2 23.1 + - - +
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Residues in contact with ILE 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C LEU* 5.0 7.0 - - + -
581D ILE* 5.7 3.4 - - + -
582D PRO 4.3 4.5 - - - +
583D GLY* 3.1 44.0 - - - +
584D PHE* 3.9 1.6 - - - +
587D LEU* 3.9 15.3 - - + -
672D LEU* 4.5 11.2 - - + -
685D LEU* 2.7 34.3 + - + +
686D PHE* 3.5 6.7 - - - +
687D ASP 2.9 0.4 + - - -
688D GLU* 1.3 73.2 - - - +
690D ARG* 1.3 69.8 + - - +
691D MET 2.9 2.4 + - - -
692D THR* 3.0 23.4 + - - -
693D TYR* 3.2 29.0 + - + -
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Residues in contact with ARG 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669D LEU* 4.1 6.9 + - + +
672D LEU* 3.0 55.6 + - + +
673D SER* 4.3 7.1 + - - +
686D PHE* 2.9 21.9 + - + +
687D ASP* 2.8 17.2 + - - +
689D ILE* 1.3 71.3 - - - +
691D MET* 1.3 63.7 + - - +
693D TYR* 3.1 5.4 + - - +
694D ILE* 3.0 50.4 + - + +
772D LEU* 3.3 33.5 + - - +
773D LEU 5.3 4.2 + - - +
774D PHE* 3.0 40.8 - - - -
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Residues in contact with MET 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687D ASP 2.6 15.5 + - - +
688D GLU* 3.0 19.7 - - - +
689D ILE 2.9 0.8 + - - -
690D ARG* 1.3 72.2 - - - +
692D THR* 1.3 53.9 + - + +
694D ILE* 2.8 34.9 + - + +
695D LYS* 2.7 53.0 + - + +
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Residues in contact with THR 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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528C LEU* 4.4 18.5 - - + +
532D LEU* 4.7 6.6 - - - +
688D GLU* 3.3 32.1 - - - +
689D ILE* 3.0 14.8 + - - -
691D MET* 1.3 77.2 - - + +
693D TYR* 1.3 64.6 + - - +
695D LYS* 3.2 11.8 - - - +
696D GLU* 2.6 35.8 + - - +
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Residues in contact with TYR 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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528C LEU* 3.6 16.5 - - + +
532D LEU* 3.6 22.4 - - + +
536D LEU* 3.5 30.9 - - + +
581D ILE* 4.5 10.5 - - + -
582D PRO* 3.4 29.3 - - - +
665D CYS* 4.4 5.5 - - - +
668D THR* 3.6 25.8 - - + -
669D LEU* 4.2 20.0 - - + +
672D LEU* 4.7 1.8 - - + -
689D ILE* 3.2 36.5 + - + +
690D ARG* 3.1 10.2 + - - +
691D MET 2.9 1.0 + - - -
692D THR* 1.3 84.9 + - - +
694D ILE* 1.3 64.3 + - - +
695D LYS 3.1 1.3 - - - -
696D GLU* 3.7 11.9 - - + +
697D LEU* 3.2 20.4 + - - +
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Residues in contact with ILE 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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669D LEU* 3.9 20.2 - - + -
690D ARG* 3.0 50.5 + - + +
691D MET* 2.8 25.0 + - + +
693D TYR* 1.3 77.6 - - - +
695D LYS* 1.3 65.0 + - + +
697D LEU* 3.5 9.2 - - + +
698D GLY* 3.5 12.1 + - - -
715D PHE* 4.2 28.9 - - + -
774D PHE* 4.4 13.7 - - + -
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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 MET* 2.7 52.0 - - + +
692D THR* 3.2 10.3 - - - +
694D ILE* 1.3 79.2 - - + +
696D GLU* 1.3 55.6 + - - +
697D LEU 2.9 4.3 - - - -
698D GLY* 2.6 29.1 + - - +
699D LYS* 3.3 12.0 + - + +
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Residues in contact with GLU 696 (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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531D THR* 3.9 1.4 - - - +
532D LEU* 2.7 43.0 - - + +
533D VAL* 2.9 26.6 - - + +
536D LEU* 4.9 0.7 - - + -
665D CYS* 3.9 10.8 - - - -
692D THR 2.6 21.4 + - - +
693D TYR* 3.9 20.6 - - + +
695D LYS* 1.3 72.3 - - - +
697D LEU* 1.3 60.9 + - - +
699D LYS* 2.5 45.3 + - - +
700D ALA* 3.5 16.5 + - - +
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Residues in contact with LEU 697 (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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662D GLU* 3.7 39.0 - - + +
665D CYS* 4.0 11.6 - - + +
666D MET* 3.9 14.4 - - + -
669D LEU* 3.6 26.5 - - + -
693D TYR 3.2 13.1 + - - +
694D ILE* 3.5 12.8 - - + +
695D LYS 2.9 0.8 + - - -
696D GLU* 1.3 77.9 - - - +
698D GLY* 1.3 57.8 + - - +
700D ALA* 2.9 26.2 + - - +
701D ILE* 3.2 14.5 + - + +
715D PHE* 5.1 10.8 - - + -
718D LEU* 4.2 17.9 - - + -
719D THR* 5.5 6.3 - - - +
722D LEU* 5.2 2.7 - - + -
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Residues in contact with GLY 698 (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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694D ILE 3.5 4.6 + - - -
695D LYS 2.6 17.1 + - - -
697D LEU* 1.3 75.1 - - - +
699D LYS* 1.3 56.8 + - - -
701D ILE* 3.3 13.6 + - - +
702D VAL* 2.9 30.1 + - - +
715D PHE* 5.1 9.2 - - - -
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Residues in contact with LYS 699 (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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531D THR* 3.8 15.0 - - - +
695D LYS* 3.6 13.7 - - + +
696D GLU* 2.5 42.9 + - - +
697D LEU 3.2 0.4 - - - -
698D GLY* 1.3 73.2 - - - +
700D ALA* 1.3 60.3 + - - +
702D VAL* 3.2 12.2 + - - +
703D LYS* 3.0 49.8 + - - +
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Residues in contact with ALA 700 (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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533D VAL* 5.4 0.2 - - + -
659D SER* 4.7 2.8 + - - -
661D GLU* 4.0 37.9 - - + +
662D GLU* 4.1 15.1 - - + +
665D CYS* 4.4 2.0 - - - -
696D GLU 3.5 9.6 + - - +
697D LEU* 2.9 15.4 + - - +
699D LYS* 1.3 79.1 - - - +
701D ILE* 1.3 58.1 + - - +
703D LYS* 3.4 34.3 - - - +
704D ARG* 4.4 0.9 + - - +
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Residues in contact with ILE 701 (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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662D GLU* 3.5 18.8 - - + +
697D LEU* 3.2 17.6 + - + +
698D GLY* 3.7 8.3 - - - +
699D LYS 3.2 0.2 - - - -
700D ALA* 1.3 73.5 - - - +
702D VAL* 1.3 62.0 + - - +
703D LYS 3.1 1.8 - - - -
704D ARG* 2.8 27.2 - - - +
711D ASN* 3.3 20.7 + - + +
714D ARG* 3.1 30.5 - - + -
715D PHE* 3.9 33.9 - - + -
718D LEU* 3.2 28.5 - - + -
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Residues in contact with VAL 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D GLY 2.9 25.1 + - - +
699D LYS* 3.2 15.0 + - - +
701D ILE* 1.3 76.7 - - - +
703D LYS* 1.3 53.8 + - + +
704D ARG 2.6 17.0 + - - -
708D SER* 3.1 21.8 + - - +
711D ASN* 3.2 18.1 - - + +
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Residues in contact with LYS 703 (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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531D THR* 5.0 3.8 - - - +
533D VAL* 3.6 29.5 - - - +
661D GLU* 2.9 33.8 + - - +
699D LYS* 3.0 34.9 - - - +
700D ALA* 3.4 20.0 - - - +
701D ILE 3.1 0.4 - - - -
702D VAL* 1.3 72.9 - - + +
704D ARG* 1.3 72.8 + - - +
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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
------------------------------------------------------------
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