Contacts of the helix formed by residues 718 - 735 (chain B) in PDB entry 3U44
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 718 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A GLN 5.6 0.2 - - - -
998A LEU* 3.8 8.1 - - - +
332B HIS* 6.1 0.7 - - + -
365B ASP 3.3 25.1 + - - +
366B TYR* 5.3 4.7 - - - +
367B GLU* 4.2 27.3 + - - +
716B VAL 3.2 1.4 + - - -
717B VAL* 1.3 85.5 - - + +
719B LYS* 1.3 73.5 + - - +
720B SER* 3.4 20.5 + - - -
721B VAL* 3.1 11.3 - - + +
722B ALA* 2.7 36.6 + - - +
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Residues in contact with LYS 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LYS* 4.1 13.7 - - - +
998A LEU* 3.8 18.5 + - + +
718B ASN* 1.3 82.7 + - - +
720B SER* 1.3 74.2 + - - +
722B ALA* 3.4 2.1 - - - +
723B GLN* 2.7 65.2 + - - +
750B LEU* 3.9 20.6 - - + -
753B GLU* 4.6 6.5 - - - +
755B ASP* 3.4 26.1 + - - +
758B GLN* 4.9 7.1 - - - +
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Residues in contact with SER 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LYS* 4.1 17.8 + - - +
725A ASP* 4.8 3.3 - - - +
365B ASP* 5.3 5.4 - - - -
718B ASN* 3.4 16.0 + - - -
719B LYS* 1.3 87.7 - - - +
721B VAL* 1.3 60.1 + - - +
723B GLN* 3.2 14.1 + - - +
724B SER* 2.9 28.7 + - - -
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Residues in contact with VAL 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 5.7 0.2 - - - +
365B ASP* 4.5 19.1 - - + +
366B TYR* 3.9 36.8 - - + -
715B TYR 3.6 8.3 - - - +
717B VAL* 3.3 16.6 - - + -
718B ASN* 3.1 31.4 - - + +
720B SER* 1.3 73.5 - - - +
722B ALA* 1.3 69.3 + - - +
724B SER* 3.4 6.9 + - - -
725B PHE* 3.0 37.7 + - + -
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Residues in contact with ALA 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A LEU* 3.9 15.0 - - + -
715B TYR 4.2 6.7 - - - -
716B VAL* 4.3 8.7 - - - +
718B ASN 2.7 23.5 + - - +
719B LYS 3.4 4.0 - - - +
721B VAL* 1.3 75.0 - - - +
723B GLN* 1.3 57.3 + - - +
725B PHE* 3.8 3.4 - - - +
726B THR* 2.9 35.8 + - - +
743B TRP* 5.0 1.8 - - - -
746B THR* 3.8 22.9 - - + -
750B LEU* 4.7 3.4 - - + -
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Residues in contact with GLN 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LYS* 3.3 20.0 - - - +
719B LYS* 2.7 55.4 + - - +
720B SER* 3.3 10.4 - - - +
722B ALA* 1.3 73.6 - - - +
724B SER* 1.3 67.4 + - - +
726B THR* 2.8 22.5 + - - -
727B ALA* 2.9 14.4 + - - +
750B LEU* 3.8 19.2 - - + +
755B ASP* 5.2 1.4 + - - -
758B GLN* 5.5 3.0 - - - +
759B SER* 3.0 33.4 + - - +
762B LEU* 3.5 22.1 - - + +
763B PHE* 4.7 0.9 - - + -
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Residues in contact with SER 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ASP* 2.7 48.5 + - - +
737A GLN* 4.8 8.1 + - - -
720B SER 2.9 15.5 + - - -
721B VAL* 3.4 8.7 + - - -
723B GLN* 1.3 75.5 - - - +
725B PHE* 1.3 64.5 + - - +
727B ALA* 4.1 2.9 - - - +
728B SER* 3.6 18.2 + - - -
762B LEU* 4.5 0.2 - - - +
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Residues in contact with PHE 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 4.1 5.8 - - - -
329B ARG* 3.5 9.4 - - - -
366B TYR* 3.8 17.3 - - - -
702B ASN* 3.5 37.9 - - + -
704B PRO* 3.5 21.1 - - + -
715B TYR* 3.4 35.2 - + + -
721B VAL* 3.0 34.7 + - + +
722B ALA 3.8 0.2 - - - +
723B GLN 3.0 0.6 - - - -
724B SER* 1.3 81.7 - - - +
726B THR* 1.3 59.5 + - - +
727B ALA 3.3 0.2 - - - -
728B SER* 2.6 23.5 + - - -
729B GLN* 2.9 19.7 + - - +
743B TRP* 3.5 22.9 - + + -
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Residues in contact with THR 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ALA 2.9 22.4 + - - +
723B GLN* 2.8 19.9 + - - -
725B PHE* 1.3 73.8 - - - +
727B ALA* 1.3 66.6 + - - +
729B GLN* 3.0 4.6 + - - +
730B LEU* 2.9 32.9 + - - +
743B TRP* 3.4 35.2 - - + +
746B THR* 3.4 25.6 - - + -
747B TYR* 4.7 4.7 - - - +
750B LEU* 4.3 1.6 - - + +
763B PHE* 3.0 25.0 - - - -
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Residues in contact with ALA 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A ASP 4.1 19.1 - - - +
729A GLY* 3.7 9.3 - - - -
723B GLN 2.9 15.5 + - - +
724B SER 4.1 2.9 - - - +
726B THR* 1.3 79.3 + - - +
728B SER* 1.3 61.0 + - - +
730B LEU* 3.6 4.1 + - - +
731B ARG* 3.3 19.8 + - - +
762B LEU* 4.3 12.6 - - + -
763B PHE* 3.4 24.0 - - + -
765B SER* 4.8 8.5 - - - +
766B LEU* 4.7 1.6 - - - +
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Residues in contact with SER 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A GLY* 3.5 24.6 + - - +
737A GLN* 5.1 8.5 - - - -
702B ASN 5.6 1.0 + - - -
704B PRO* 5.6 1.2 - - - +
724B SER 3.6 9.8 + - - -
725B PHE* 2.6 30.7 + - - -
727B ALA* 1.3 78.2 - - - +
729B GLN* 1.3 68.9 + - - +
731B ARG* 3.5 2.8 - - - +
732B LEU* 3.2 23.7 + - - +
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Residues in contact with GLN 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B PRO* 4.0 17.5 - - + +
705B GLU* 3.1 34.6 + - - +
712B GLN* 5.2 0.7 + - - -
725B PHE 2.9 16.4 + - - +
726B THR* 3.0 10.7 + - - +
728B SER* 1.3 80.3 + - - +
730B LEU* 1.3 60.7 + - + +
732B LEU* 3.4 6.9 + - - +
733B TRP* 2.9 30.3 + - - +
739B ILE* 3.8 28.0 - - + +
740B SER 4.8 0.7 + - - -
743B TRP* 3.4 53.2 + - + +
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Residues in contact with LEU 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A ILE* 4.6 7.9 - - + -
726B THR* 2.9 21.0 + - - +
727B ALA* 3.9 2.5 - - - +
729B GLN* 1.3 76.5 - - + +
731B ARG* 1.3 65.7 + - - +
733B TRP* 3.2 9.4 + - + +
734B THR* 3.1 24.9 + - - +
739B ILE* 4.9 5.4 - - + -
743B TRP* 5.4 7.4 - - + +
744B TRP* 4.2 30.1 - - + -
747B TYR* 4.0 26.9 - - + -
763B PHE* 3.8 30.7 - - + -
766B LEU* 3.5 31.0 - - + -
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Residues in contact with ARG 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A GLY 3.6 19.7 - - - +
729A GLY* 3.1 16.4 + - - -
730A MET* 3.2 19.9 - - - +
731A PRO* 3.0 37.8 - - + +
732A GLY 5.5 0.2 - - - +
733A GLY* 5.3 2.7 - - - +
734A LYS* 6.5 0.4 - - + -
727B ALA 3.3 7.7 + - - +
728B SER 3.5 9.9 - - - +
730B LEU* 1.3 78.3 - - - +
732B LEU* 1.3 61.0 + - - +
733B TRP 2.9 5.5 + - - -
734B THR* 2.8 48.4 + - - +
735B ARG* 3.5 16.5 + - - +
766B LEU* 2.6 37.6 + - - +
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Residues in contact with LEU 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A LYS* 4.8 12.6 - - + +
705B GLU* 3.6 33.4 - - + +
728B SER 3.2 13.4 + - - +
729B GLN* 4.0 6.5 - - - +
731B ARG* 1.3 79.5 - - - +
733B TRP* 1.3 60.8 + - - +
735B ARG* 3.3 51.9 - - - +
737B TYR* 3.2 52.6 - - + +
739B ILE* 4.4 5.4 - - + -
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Residues in contact with TRP 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A SER 6.0 1.1 - - - -
974A ARG* 3.9 32.0 - - + +
975A LEU* 4.0 27.6 - - + -
978A ILE* 4.6 7.0 - - + -
729B GLN 2.9 18.7 + - - +
730B LEU* 3.2 20.4 - - + +
731B ARG 2.9 0.2 + - - -
732B LEU* 1.3 74.0 - - - +
734B THR* 1.3 73.6 + - + +
735B ARG 2.9 6.4 + - - -
736B GLU* 2.9 13.7 + - - -
737B TYR 3.2 27.5 + - - -
738B ASP* 4.8 3.4 + - - +
739B ILE* 3.7 29.1 - - + +
744B TRP* 3.4 38.2 - + - -
766B LEU* 5.7 0.4 - - + -
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Residues in contact with THR 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A LEU* 4.7 18.6 - - + -
730B LEU 3.2 14.6 - - - +
731B ARG* 2.8 35.7 + - - +
733B TRP* 1.3 89.3 - - + +
735B ARG* 1.3 56.6 + - - +
736B GLU* 2.9 15.3 + - - +
766B LEU* 4.2 20.0 - - + -
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Residues in contact with ARG 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A ARG* 6.2 2.0 - - - +
608A PRO* 5.6 11.0 - - - +
731A PRO* 6.1 2.6 - - - +
732A GLY* 5.4 8.8 - - - +
733A GLY 6.0 0.8 - - - +
734A LYS* 4.1 23.1 - - - +
731B ARG* 4.2 16.3 - - - +
732B LEU* 3.3 61.5 + - - +
733B TRP 2.9 1.6 - - - -
734B THR* 1.3 80.0 + - - +
736B GLU* 1.3 65.5 + - - +
737B TYR* 3.2 9.3 + - + +
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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