Contacts of the helix formed by residues 689 - 703 (chain D) in PDB entry 5UHG
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 HIS 689 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586D TYR* 3.5 15.5 - + + -
687D GLN* 3.0 12.1 + - + +
688D MET* 1.3 78.1 - - - +
690D LYS* 1.3 69.8 + - + +
691D LYS* 2.9 53.5 + - + +
692D VAL* 3.1 22.2 + - + +
693D GLN* 3.2 10.4 + - - +
803D VAL 5.3 0.4 + - - -
804D ASP 3.3 22.2 + - - -
805D SER* 3.3 15.9 - - - -
806D GLY* 3.6 17.9 + - - -
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Residues in contact with LYS 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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576D MET* 4.2 18.8 - - - -
577D PRO 4.6 13.5 - - - +
578D ARG* 4.8 8.0 + - - +
582D VAL* 4.3 10.7 - - + +
688D MET 3.9 0.2 + - - -
689D HIS* 1.3 80.1 + - + +
691D LYS* 1.3 62.0 + - - +
693D GLN* 3.2 8.8 + - + +
694D ALA* 2.8 28.8 + - + +
805D SER 3.3 8.2 + - - +
806D GLY* 3.3 33.5 + - - +
807D ALA 5.4 1.0 + - - -
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Residues in contact with LYS 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689D HIS* 2.9 27.5 + - + +
690D LYS* 1.3 81.0 - - + +
692D VAL* 1.3 64.9 + - + +
694D ALA* 3.3 10.0 - - - +
695D ALA* 3.2 21.1 + - - +
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Residues in contact with VAL 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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684D VAL* 6.3 0.9 - - + -
686D LYS* 4.9 17.3 - - + -
687D GLN 3.7 16.8 - - - +
688D MET* 3.7 30.7 - - + -
689D HIS* 3.1 22.6 + - + +
691D LYS* 1.3 78.0 - - + +
693D GLN* 1.3 62.8 + - - +
695D ALA* 2.9 18.2 + - - +
696D ILE* 3.2 17.2 + - + +
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Residues in contact with GLN 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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576D MET* 5.1 4.5 - - - -
577D PRO* 3.5 23.7 - - + +
582D VAL* 3.8 18.0 + - - +
585D LEU* 3.2 36.5 - - - +
673D PHE* 5.3 3.1 - - + -
688D MET* 2.9 47.1 + - + +
689D HIS 3.3 10.4 + - - +
690D LYS* 3.2 6.4 + - - +
692D VAL* 1.3 75.9 - - - +
694D ALA* 1.3 61.0 + - - +
696D ILE* 3.4 12.7 + - + +
697D ILE* 3.2 32.3 + - + +
716D LEU* 5.6 3.9 - - + +
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Residues in contact with ALA 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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573D PRO* 3.9 8.9 - - + +
576D MET* 3.6 29.8 - - + -
690D LYS* 2.8 13.9 + - + +
691D LYS* 3.3 15.3 - - - +
693D GLN* 1.3 78.7 - - - +
695D ALA* 1.3 57.3 + - - +
697D ILE 3.6 0.2 + - - -
698D ASN* 3.0 30.9 + - - +
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Residues in contact with ALA 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 LYS 3.2 8.4 + - - +
692D VAL* 2.9 11.9 + - - +
694D ALA* 1.3 77.7 - - - +
696D ILE* 1.3 59.8 + - + +
698D ASN* 3.7 5.9 - - - +
699D ASP* 2.9 30.9 + - - +
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Residues in contact with ILE 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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673D PHE* 4.0 31.4 - - + -
677D LEU* 4.1 20.9 - - + -
681D TYR* 4.0 21.4 + - + +
684D VAL* 4.2 22.4 - - + -
688D MET* 4.2 10.5 - - - -
692D VAL* 3.2 16.5 + - + +
693D GLN* 3.7 9.4 - - - +
694D ALA 3.3 0.2 - - - -
695D ALA* 1.3 76.5 - - + +
697D ILE* 1.3 60.3 + - + +
699D ASP* 3.2 4.9 + - - +
700D LEU* 2.9 46.2 + - + +
716D LEU* 6.0 2.2 - - + -
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Residues in contact with ILE 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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565D ILE* 5.4 5.6 - - + -
566D LEU* 5.9 1.3 - - + -
573D PRO* 4.2 17.5 - - + -
575D ALA 5.6 0.2 - - - +
576D MET* 3.8 28.5 - - + -
577D PRO* 4.0 14.6 - - + -
693D GLN* 3.2 18.3 + - + +
694D ALA 4.1 2.9 - - - +
696D ILE* 1.3 77.0 - - + +
698D ASN* 1.3 52.9 + - - +
700D LEU* 3.0 14.4 + - + +
701D ALA* 2.8 35.1 + - + +
709D VAL* 4.1 22.2 - - + +
712D THR* 6.3 0.4 - - + -
713D VAL* 4.1 17.3 - - + -
716D LEU* 4.3 16.8 - - + -
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Residues in contact with ASN 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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566D LEU* 5.3 1.7 - - - +
571D GLY 4.1 16.6 + - - +
572D ARG* 4.4 8.1 - - - +
573D PRO* 4.0 22.5 - - + +
694D ALA 3.0 18.8 + - - +
695D ALA* 3.7 7.0 - - - +
697D ILE* 1.3 77.4 - - - +
699D ASP* 1.3 60.7 + - - +
701D ALA* 3.4 9.9 - - - +
702D GLU* 3.4 28.4 + - - +
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Residues in contact with ASP 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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681D TYR* 3.2 24.1 + - - +
695D ALA 2.9 14.3 + - - +
696D ILE 3.4 8.7 - - - +
698D ASN* 1.3 75.6 - - - +
700D LEU* 1.3 64.4 + - - +
701D ALA 3.1 0.2 - - - -
702D GLU* 3.1 18.2 + - - +
703D ARG* 3.2 49.3 + - - +
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Residues in contact with LEU 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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677D LEU* 4.0 16.8 - - + +
681D TYR* 3.8 22.2 - - + -
696D ILE* 2.9 31.0 + - + +
697D ILE* 3.0 19.9 + - + +
699D ASP* 1.3 76.6 - - - +
701D ALA* 1.3 58.4 + - - +
704D TYR* 2.8 61.7 + - + +
708D VAL* 5.4 2.0 - - + -
709D VAL* 3.3 18.4 - - + +
712D THR* 3.9 29.2 - - + +
716D LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 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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566D LEU* 4.0 32.3 - - + -
697D ILE* 2.8 13.2 + - + +
698D ASN* 3.4 16.6 - - - +
699D ASP 3.1 0.2 - - - -
700D LEU* 1.3 79.0 - - - +
702D GLU* 1.3 63.5 + - + +
704D TYR 3.9 5.5 - - - +
709D VAL* 4.0 12.8 - - + +
985D THR 5.5 2.9 - - - +
986D GLY* 5.9 2.5 - - - -
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Residues in contact with GLU 702 (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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698D ASN* 3.4 22.2 - - - +
699D ASP* 3.1 13.8 + - - +
701D ALA* 1.3 80.6 - - + +
703D ARG* 1.3 69.8 + - + +
945D GLY* 5.8 1.1 - - - -
946D ASP* 5.0 16.7 + - + +
981D ARG* 3.1 31.2 + - - -
986D GLY* 4.8 8.2 - - - +
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Residues in contact with ARG 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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641D ARG* 5.7 2.6 - - - +
680D GLY 4.3 2.6 + - - -
681D TYR* 4.2 9.0 - - - -
682D PRO* 4.2 17.8 - - - +
699D ASP* 3.2 40.2 + - - +
702D GLU* 1.3 84.6 - - + +
704D TYR* 1.3 104.3 + - + +
705D PRO* 3.7 3.8 - - - +
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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
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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