Contacts of the helix formed by residues 703 - 718 (chain D) in PDB entry 1UES
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 703 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697D ILE* 4.0 3.8 - - - +
698D ASP* 3.7 14.5 + - - +
701D PHE* 3.2 5.5 + - - +
702D GLY* 1.3 80.6 - - - +
704D PHE* 1.3 64.2 + - - +
705D GLU* 3.4 8.3 + - - +
706D LYS* 3.0 30.9 + - - +
707D PHE* 3.0 22.7 + - - +
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Residues in contact with PHE 704 (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 GLY 3.5 22.0 - - - -
688D ALA* 3.7 19.3 - - + -
689D PRO* 3.5 31.2 - - + -
697D ILE* 4.0 10.1 - - + -
698D ASP* 3.6 11.8 + - - +
703D SER* 1.3 73.4 - - - +
705D GLU* 1.3 64.9 + - + +
707D PHE* 3.1 16.0 + + - +
708D LYS* 2.9 65.6 + - + +
779D TRP* 4.3 5.6 - + + -
784D TRP* 3.6 26.5 - + - -
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Residues in contact with GLU 705 (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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703D SER* 3.2 6.9 + - - +
704D PHE* 1.3 83.2 - - + +
706D LYS* 1.3 65.0 + - + +
708D LYS* 2.8 40.8 + - - +
709D GLU* 3.1 23.9 + - - +
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Residues in contact with LYS 706 (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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61A GLU* 3.4 28.9 + - - +
701D PHE* 3.2 26.7 - - - +
702D GLY* 3.8 12.3 - - - -
703D SER* 3.0 23.2 + - - +
705D GLU* 1.3 75.5 - - - +
707D PHE* 1.3 63.9 + - - +
709D GLU* 3.2 15.4 + - - +
710D GLU* 3.1 31.2 + - + +
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Residues in contact with PHE 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D ILE* 3.7 20.9 - - + -
701D PHE* 3.8 36.2 - + + +
703D SER 3.0 13.8 + - - +
704D PHE* 3.1 23.1 + + - +
706D LYS* 1.3 77.1 - - - +
708D LYS* 1.3 65.2 + - - +
710D GLU* 3.2 3.7 + - - +
711D PHE* 2.9 52.5 + + - +
726D LEU* 3.9 34.5 - - + -
736D ILE* 4.0 8.5 - - + -
754D LEU* 4.4 1.8 - - + -
779D TRP* 3.5 26.9 - + - -
784D TRP* 4.2 11.2 - + - -
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Residues in contact with LYS 708 (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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704D PHE* 2.9 54.9 + - + +
705D GLU* 2.8 40.3 + - - +
706D LYS 3.3 0.2 - - - -
707D PHE* 1.3 76.3 - - - +
709D GLU* 1.3 58.0 + - - +
711D PHE* 3.3 0.9 + - - +
712D ASN* 2.8 39.5 + - - +
779D TRP* 3.8 54.2 - - + +
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Residues in contact with GLU 709 (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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47A GLU* 3.7 21.7 - - - +
48A PHE* 5.4 9.0 - - + -
61A GLU* 4.4 20.4 - - - +
705D GLU 3.1 16.4 + - - +
706D LYS* 3.6 15.4 - - - +
707D PHE 3.2 0.2 - - - -
708D LYS* 1.3 77.9 - - - +
710D GLU* 1.3 72.8 + - - +
712D ASN* 3.7 1.6 - - - +
713D THR* 2.9 40.4 + - - +
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Residues in contact with GLU 710 (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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701D PHE* 3.7 36.4 - - - +
706D LYS* 3.1 16.9 + - - +
707D PHE 3.6 7.2 - - - +
709D GLU* 1.3 88.4 - - - +
711D PHE* 1.3 57.3 + - - +
713D THR* 3.3 6.6 + - - +
714D ALA* 2.9 29.6 + - - +
736D ILE* 3.7 13.4 - - + +
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Residues in contact with PHE 711 (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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707D PHE* 2.9 33.9 + + + +
708D LYS 3.6 4.0 - - - +
710D GLU* 1.3 74.9 - - - +
712D ASN* 1.3 64.8 + - - +
714D ALA* 3.3 5.0 + - - +
715D GLY* 3.1 18.7 + - - -
724D VAL* 3.5 38.8 - - + +
725D TRP 3.5 24.7 - - - -
726D LEU* 3.5 10.5 - - + -
736D ILE* 3.8 10.9 - - + +
754D LEU* 3.7 23.8 - - + -
756D PHE* 3.6 34.5 - + - -
779D TRP* 3.5 27.4 - + + -
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Residues in contact with ASN 712 (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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47A GLU* 3.1 42.5 + - + +
708D LYS* 2.8 27.6 + - - +
709D GLU* 3.7 0.6 - - - +
711D PHE* 1.3 73.4 - - - +
713D THR* 1.3 59.0 + - - +
715D GLY* 3.2 1.7 + - - -
716D THR* 2.8 35.4 + - - +
756D PHE* 4.3 1.6 - - - -
775D LEU* 3.8 24.9 - - + +
776D LYS* 4.1 11.9 - - + +
779D TRP* 2.8 32.3 + - - +
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Residues in contact with THR 713 (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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45A GLY 3.2 14.9 - - - +
46A THR* 3.9 27.4 - - + +
47A GLU* 4.5 2.6 + - - -
709D GLU* 2.9 27.9 + - - +
710D GLU* 3.7 7.2 - - - +
712D ASN* 1.3 78.9 - - - +
714D ALA* 1.3 56.2 + - - +
717D THR* 2.8 42.2 + - - +
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Residues in contact with ALA 714 (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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710D GLU 2.9 17.1 + - - +
711D PHE 3.6 4.9 - - - +
713D THR* 1.3 75.8 - - - +
715D GLY* 1.3 61.6 + - - +
717D THR* 4.7 1.3 - - - -
718D LEU* 3.2 20.1 + - - +
724D VAL* 3.7 7.2 - - + -
736D ILE* 3.7 26.0 - - + -
738D LYS* 3.3 34.2 - - + +
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Residues in contact with GLY 715 (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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711D PHE 3.1 10.9 + - - -
712D ASN 3.7 2.2 - - - -
714D ALA* 1.3 79.1 - - - +
716D THR* 1.3 56.7 + - - +
718D LEU* 3.7 5.9 + - - +
724D VAL* 3.9 22.1 - - - +
758D VAL* 3.7 7.9 - - - +
771D ARG* 2.9 27.0 + - - -
775D LEU* 3.6 16.6 - - - -
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Residues in contact with THR 716 (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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45A GLY* 3.3 29.4 - - - -
46A THR 3.6 12.0 - - - +
47A GLU* 4.4 1.6 + - - -
49A GLU* 3.6 26.6 - - - +
712D ASN* 2.8 18.0 + - - +
715D GLY* 1.3 75.5 - - - +
717D THR* 1.3 61.5 + - - +
718D LEU 3.7 0.5 + - - +
771D ARG* 3.7 19.1 + - + +
772D ALA* 3.9 20.7 - - + +
775D LEU* 3.5 12.0 - - - +
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Residues in contact with THR 717 (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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44A ILE 4.9 0.7 + - - -
45A GLY* 2.9 28.3 + - - -
713D THR* 2.8 24.1 + - - +
714D ALA* 4.0 3.6 - - - -
716D THR* 1.3 77.2 - - - +
718D LEU* 1.3 65.6 + - - +
719D PHE* 2.9 8.8 + - - +
738D LYS* 3.8 21.5 - - - +
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Residues in contact with LEU 718 (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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714D ALA 3.2 15.8 + - - +
715D GLY* 3.8 9.0 - - - +
716D THR 3.4 1.3 - - - +
717D THR* 1.3 74.0 - - - +
719D PHE* 1.3 75.1 + - - +
720D GLY 3.6 7.9 + - - +
721D SER 3.5 26.9 - - - +
722D GLY* 3.9 1.8 - - - +
723D TRP 3.4 39.7 - - - +
724D VAL* 5.1 0.9 - - + -
738D LYS* 4.2 19.5 - - + +
739D GLU 3.8 15.3 - - - +
740D PRO* 4.5 10.3 - - + -
758D VAL* 4.1 4.5 - - + -
771D ARG* 2.7 27.6 + - - +
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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