Contacts of the helix formed by residues 711 - 727 (chain C) 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 711 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700C GLN* 3.1 25.5 - - - +
710C GLN* 1.3 77.9 - - - +
712C ASN* 1.3 83.8 + - - +
714C TRP* 2.8 18.0 + - - +
715C THR* 3.1 29.0 + - - +
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Residues in contact with ASN 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710C GLN 3.4 5.7 + - - +
711C ASN* 1.3 87.0 + - - +
713C GLN* 1.3 56.3 + - - +
715C THR* 3.1 10.8 + - - -
716C GLU* 2.8 35.1 + - - +
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Residues in contact with GLN 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C VAL 5.7 0.2 - - - +
653C THR* 3.4 22.2 - - + +
654C SER* 5.3 0.3 + - - -
657C ARG* 3.3 40.4 + - + +
710C GLN* 3.2 21.1 + - - +
711C ASN 3.0 0.8 - - - -
712C ASN* 1.3 79.6 - - - +
714C TRP* 1.3 61.0 + - - +
716C GLU* 3.4 5.0 - - - +
717C VAL* 3.1 29.1 + - + +
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Residues in contact with TRP 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C SER* 5.2 6.1 - - - +
652C ILE* 3.6 20.6 - - + -
653C THR* 3.7 27.9 - - - +
656C LEU* 3.5 26.7 - - + -
692C LEU 4.1 6.3 - - - -
693C LEU* 4.2 4.7 - - - -
696C GLY* 3.3 39.7 + - - -
700C GLN* 3.2 38.2 - - + +
710C GLN 3.7 4.1 + - - +
711C ASN* 2.8 14.6 + - - +
713C GLN* 1.3 71.6 - - - +
715C THR* 1.3 79.6 + - + +
717C VAL* 3.0 14.5 + - + +
718C MET* 2.9 47.4 + - + +
746C LEU* 4.9 4.2 - - + +
750C TYR* 3.4 20.4 + - - -
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Residues in contact with THR 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700C GLN* 4.5 0.7 - - + +
711C ASN* 3.1 29.9 + - - +
712C ASN* 3.1 21.7 + - - -
714C TRP* 1.3 83.6 - - + +
716C GLU* 1.3 55.5 + - - +
718C MET* 3.2 3.0 + - - +
719C PHE* 2.9 45.1 + - - -
750C TYR* 3.7 26.4 - - + +
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Residues in contact with GLU 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C LEU* 5.0 5.6 - - + -
712C ASN* 2.8 21.3 + - - +
713C GLN* 3.4 8.3 - - - +
714C TRP 3.0 0.2 + - - -
715C THR* 1.3 80.9 + - - +
717C VAL* 1.3 62.4 + - + +
718C MET 3.3 0.7 + - - -
719C PHE* 3.3 17.3 + - - +
720C MET* 3.2 49.9 + - + +
723C ARG* 4.9 6.8 + - - -
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Residues in contact with VAL 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C THR* 4.8 4.3 - - + -
656C LEU* 3.7 33.2 - - + -
657C ARG* 4.1 21.8 - - + +
660C MET* 2.8 46.2 - - - +
662C LEU* 4.0 21.1 - - + -
713C GLN* 3.1 15.9 - - + +
714C TRP* 3.0 26.4 + - + +
716C GLU* 1.3 76.4 - - + +
718C MET* 1.3 56.7 + - - +
720C MET* 3.9 4.9 - - - -
721C ALA* 3.1 5.4 + - - +
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Residues in contact with MET 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C LEU* 4.4 1.8 - - + -
693C LEU* 3.7 22.9 - - + -
714C TRP* 2.9 55.8 + - + +
715C THR 3.4 8.7 - - - +
716C GLU 3.1 0.2 - - - -
717C VAL* 1.3 75.0 - - - +
719C PHE* 1.3 65.4 + - - +
720C MET 3.1 2.0 - - - -
721C ALA* 3.8 2.8 - - - +
722C THR* 3.0 38.6 + - + +
746C LEU* 3.7 28.5 - - + -
747C PHE* 5.0 0.2 - - - -
750C TYR* 3.1 34.5 - - + +
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Residues in contact with PHE 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715C THR* 2.9 37.9 + - - -
716C GLU* 3.3 15.9 + - - +
718C MET* 1.3 75.8 - - - +
720C MET* 1.3 56.9 + - - +
722C THR* 2.7 20.3 + - - -
723C ARG* 2.9 52.7 + - - +
749C ARG 5.6 2.0 - - - -
750C TYR* 3.6 42.2 - + + -
751C VAL* 5.5 2.2 - - + -
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Residues in contact with MET 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C MET* 3.7 20.2 - - - +
662C LEU* 3.9 37.2 - - + -
674C PRO* 4.3 15.9 - - + -
716C GLU* 3.2 50.0 + - + +
717C VAL* 3.9 0.9 - - - +
718C MET 3.1 0.4 - - - -
719C PHE* 1.3 75.2 - - - +
721C ALA* 1.3 65.1 + - - +
722C THR 3.2 0.2 - - - -
723C ARG* 3.7 23.4 - - - +
724C GLU* 3.0 31.6 + - - +
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Residues in contact with ALA 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660C MET* 2.9 29.0 - - + +
676C LEU* 4.5 11.5 - - + +
689C LEU* 5.0 3.6 - - + -
693C LEU* 4.2 31.6 - - + -
717C VAL 3.1 6.6 + - - +
718C MET* 3.2 4.9 + - - +
720C MET* 1.3 75.8 - - - +
722C THR* 1.3 59.2 + - + +
724C GLU* 3.8 1.4 - - - +
725C LEU* 2.9 37.0 + - + +
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Residues in contact with THR 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C MET* 3.0 20.5 + - + +
719C PHE* 2.7 26.5 + - - -
721C ALA* 1.3 73.1 - - - +
723C ARG* 1.3 58.2 + - - +
724C GLU 3.0 4.7 - - - -
725C LEU* 3.0 8.1 + - - +
726C LEU* 2.9 37.8 + - - +
747C PHE* 3.3 37.2 - - + -
750C TYR* 4.3 15.2 - - + +
751C VAL* 4.2 20.6 - - + +
759C LEU* 5.1 4.0 - - - -
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Residues in contact with ARG 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C GLU* 4.9 6.9 + - - -
719C PHE* 2.9 48.0 + - - +
720C MET* 3.4 28.1 + - - +
722C THR* 1.3 83.4 + - - +
724C GLU* 1.3 57.5 + - - +
726C LEU* 3.8 17.0 - - + +
727C ARG* 3.3 23.7 + - - +
751C VAL* 5.7 4.5 - - + -
755C LYS* 6.4 0.4 - - - +
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Residues in contact with GLU 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660C MET* 5.7 2.1 - - - +
674C PRO* 4.8 7.2 - - - +
675C HIS* 3.9 13.1 + - - +
676C LEU* 3.5 46.0 + - + +
677C THR* 4.2 11.3 + - - +
680C LEU* 3.7 8.8 - - + +
720C MET* 3.0 20.1 + - - +
721C ALA 4.1 2.0 - - - +
723C ARG* 1.3 75.5 - - - +
725C LEU* 1.3 60.7 + - - +
726C LEU 3.0 5.4 - - - -
727C ARG* 3.8 19.8 - - + +
728C ILE* 3.3 24.0 + - + +
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Residues in contact with LEU 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C LEU* 5.7 0.4 - - + -
680C LEU* 3.6 29.8 - - + -
686C LEU* 4.7 5.2 - - + -
689C LEU* 4.7 6.3 - - + -
690C LEU* 5.0 4.3 - - + -
693C LEU* 4.2 13.0 - - + -
721C ALA 2.9 23.7 + - - +
722C THR 3.5 5.8 - - - +
724C GLU* 1.3 76.5 - - - +
726C LEU* 1.3 51.8 + - - +
728C ILE* 3.2 9.0 - - - +
733C LEU* 4.4 15.2 - - + +
747C PHE* 3.7 33.7 - - + -
759C LEU* 3.7 20.0 - - + +
762C LYS* 2.7 26.9 + - - +
763C LEU* 4.5 17.7 - - + -
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Residues in contact with LEU 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722C THR* 2.9 24.4 + - - +
723C ARG* 3.8 17.9 - - + +
724C GLU 3.0 0.2 - - - -
725C LEU* 1.3 76.7 - - - +
727C ARG* 1.3 62.4 + - - +
728C ILE 3.1 3.2 - - - +
751C VAL* 4.6 12.1 - - + -
755C LYS* 4.0 40.4 - - + +
758C LEU* 5.3 9.2 - - + -
759C LEU* 3.4 39.0 - - + +
762C LYS* 2.6 21.7 + - - +
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Residues in contact with ARG 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C ARG 3.3 16.1 + - - +
724C GLU* 3.6 20.8 + - + +
726C LEU* 1.3 79.2 - - - +
728C ILE* 1.3 61.3 + - - +
729C PRO* 3.6 5.5 - - - +
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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