Contacts of the helix formed by residues 712 - 727 (chain B) in PDB entry 2XER
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 712 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711B ASN* 1.3 75.3 - - - +
713B GLN* 1.3 64.8 + - + +
715B THR* 3.1 23.2 + - - -
716B GLU* 3.4 9.5 + - - +
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Residues in contact with GLN 713 (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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650B VAL* 5.8 6.1 - - - +
653B THR* 3.5 25.5 + - + +
657B ARG* 3.2 25.4 + - - +
711B ASN* 3.1 21.9 - - - +
712B ASN* 1.3 84.3 - - + +
714B TRP* 1.3 60.8 + - - +
716B GLU* 3.0 9.9 + - + +
717B VAL* 2.9 33.6 + - + +
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Residues in contact with TRP 714 (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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649B SER* 2.9 29.7 + - - -
652B ILE* 3.4 23.3 - - + -
653B THR* 3.7 14.9 + - - +
656B LEU* 3.2 30.7 - - + -
692B LEU 3.6 8.1 - - - -
693B LEU* 3.9 3.4 - - - -
695B ARG 3.9 4.2 + - - -
696B GLY* 3.2 43.1 - - - -
699B LEU* 4.1 20.4 - - + +
711B ASN* 3.4 26.7 + - + +
713B GLN* 1.3 79.1 - - - +
715B THR* 1.3 57.6 - - + +
717B VAL* 3.3 8.3 - - + +
718B MET* 2.8 66.6 + - + +
750B TYR* 4.4 9.6 - - - +
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Residues in contact with THR 715 (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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711B ASN 3.3 15.9 + - - +
712B ASN* 3.1 15.3 + - - -
714B TRP* 1.3 75.5 - - + +
716B GLU* 1.3 62.2 + - - +
718B MET* 3.4 1.0 + - - +
719B PHE* 2.8 51.3 + - + -
750B TYR* 3.5 25.3 - - + +
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Residues in contact with GLU 716 (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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657B ARG* 6.3 0.7 - - + -
712B ASN 3.4 10.9 + - - +
713B GLN* 3.0 13.8 + - + +
715B THR* 1.3 80.6 + - - +
717B VAL* 1.3 71.2 + - + +
718B MET 3.2 0.7 + - - -
719B PHE* 3.2 16.5 + - - +
720B MET* 3.2 38.7 + - + +
723B ARG* 4.8 3.6 + - - -
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Residues in contact with VAL 717 (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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653B THR* 4.7 7.9 - - + +
656B LEU* 4.3 15.7 - - + -
657B ARG* 3.7 34.8 - - + +
660B MET* 4.1 11.8 - - - +
693B LEU* 4.7 1.5 - - + +
713B GLN* 2.9 21.3 + - + +
714B TRP* 3.3 37.2 - - + +
716B GLU* 1.3 79.3 - - + +
718B MET* 1.3 60.4 + - - +
719B PHE 3.4 0.2 - - - -
720B MET* 3.9 13.7 - - + +
721B ALA* 3.2 27.5 + - - +
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Residues in contact with MET 718 (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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693B LEU* 3.8 24.7 - - + -
714B TRP* 2.8 42.5 + - + +
715B THR 3.7 0.2 - - - +
716B GLU 3.1 0.2 - - - -
717B VAL* 1.3 77.6 - - - +
719B PHE* 1.3 62.4 + - - +
721B ALA* 4.5 1.3 - - + -
722B THR* 3.1 35.5 + - + +
746B LEU* 3.7 35.7 - - + -
747B PHE* 4.1 22.9 - - + -
750B TYR* 3.5 45.2 - - + +
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Residues in contact with PHE 719 (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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715B THR* 2.8 41.9 + - - +
716B GLU* 3.2 4.7 + - - +
718B MET* 1.3 74.8 - - - +
720B MET* 1.3 62.4 + - - +
722B THR* 3.3 4.8 + - - -
723B ARG* 3.1 58.7 + - - +
750B TYR* 3.4 46.9 - + + -
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Residues in contact with MET 720 (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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657B ARG* 5.9 4.9 - - + -
660B MET* 4.0 24.5 - - + -
661B ASN 4.0 20.0 - - - +
662B LEU* 5.3 4.9 - - + -
663B PRO* 3.6 32.1 - - + -
716B GLU* 3.2 34.3 + - + +
717B VAL* 4.0 13.5 - - + +
719B PHE* 1.3 76.4 - - - +
721B ALA* 1.3 65.9 + - - +
723B ARG* 3.3 17.7 + - - +
724B GLU* 3.0 28.9 + - - +
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Residues in contact with ALA 721 (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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660B MET* 3.6 18.1 - - + +
689B LEU* 5.6 2.0 - - + -
693B LEU* 4.0 33.9 - - + -
717B VAL 3.2 16.7 + - - +
718B MET* 4.1 6.1 - - + +
719B PHE 3.5 0.2 - - - -
720B MET* 1.3 79.6 - - - +
722B THR* 1.3 54.7 + - + +
724B GLU* 3.3 3.2 + - - +
725B LEU* 2.8 43.8 + - + +
747B PHE* 5.4 0.4 - - + -
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Residues in contact with THR 722 (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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718B MET* 3.1 25.7 + - + +
719B PHE* 3.3 10.6 + - - -
721B ALA* 1.3 72.7 - - - +
723B ARG* 1.3 64.3 + - - +
725B LEU* 3.6 7.4 - - - +
726B LEU* 2.7 39.0 + - - +
747B PHE* 3.7 32.8 - - + -
750B TYR* 4.7 4.6 + - + -
751B VAL* 3.7 31.4 - - + +
759B LEU* 4.7 6.7 - - + -
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Residues in contact with ARG 723 (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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663B PRO* 6.2 1.0 - - - +
716B GLU* 4.8 3.6 + - - -
719B PHE* 3.1 54.2 + - - +
720B MET* 3.3 20.0 + - - +
722B THR* 1.3 84.2 + - - +
724B GLU* 1.3 62.7 + - - +
726B LEU* 3.6 8.4 - - + +
727B ARG* 2.9 30.7 + - - +
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Residues in contact with GLU 724 (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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660B MET* 5.1 0.9 - - + -
663B PRO* 3.1 25.6 - - + +
664B GLY* 3.4 10.9 + - - -
676B LEU* 3.6 27.2 - - + +
680B LEU* 4.6 10.6 - - + +
720B MET 3.0 21.3 + - - +
721B ALA* 3.7 4.5 - - - +
723B ARG* 1.3 76.1 - - + +
725B LEU* 1.3 61.3 + - + +
726B LEU 3.1 1.8 - - - -
727B ARG* 2.4 43.3 + - - +
728B ILE* 2.9 35.2 + - - +
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Residues in contact with LEU 725 (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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680B LEU* 4.1 28.0 - - + -
686B LEU* 4.7 7.6 - - + -
689B LEU* 5.2 3.8 - - + -
690B LEU* 5.2 2.9 - - + -
693B LEU* 4.5 12.1 - - + -
721B ALA* 2.8 31.3 + - + +
722B THR 3.9 1.6 - - - +
724B GLU* 1.3 72.7 - - + +
726B LEU* 1.3 57.3 + - - +
728B ILE* 3.5 5.2 - - - +
733B LEU* 4.3 18.1 - - + +
747B PHE* 3.9 32.8 - - + -
759B LEU* 3.6 20.5 - - + +
762B LYS* 2.8 30.9 + - - +
763B LEU* 4.7 15.7 - - + -
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Residues in contact with LEU 726 (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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722B THR* 2.7 25.5 + - - +
723B ARG* 3.6 8.3 - - + +
725B LEU* 1.3 75.1 - - - +
727B ARG* 1.3 56.1 + - - +
751B VAL* 4.7 8.5 - - + -
755B LYS* 3.4 63.7 - - + +
758B LEU* 4.1 21.6 - - + +
759B LEU* 4.1 14.4 - - + +
762B LYS* 2.7 23.2 + - + +
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Residues in contact with ARG 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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663B PRO* 4.2 4.2 - - - +
664B GLY* 4.0 16.5 - - - +
723B ARG* 2.9 16.9 + - - +
724B GLU* 2.4 41.8 + - - +
726B LEU* 1.3 77.8 - - - +
728B ILE* 1.3 66.4 + - - +
729B PRO* 3.4 6.2 - - - +
762B LYS* 4.4 0.2 + - - -
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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