Contacts of the helix formed by residues 710 - 727 (chain A) 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 GLN 710 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A SER* 3.0 22.7 + - - -
650A VAL* 3.1 44.1 + - + +
653A THR* 3.0 32.6 + - - +
700A GLN* 3.6 8.5 + - - -
709A THR* 1.3 78.1 + - - +
711A ASN* 1.3 59.4 + - - +
713A GLN* 3.5 18.4 + - - +
714A TRP* 2.7 40.5 + - - +
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Residues in contact with ASN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A GLN* 5.1 6.4 - - - +
709A THR 3.2 0.4 - - - -
710A GLN* 1.3 80.4 - - - +
712A ASN* 1.3 57.9 + - - +
714A TRP* 4.7 4.1 - - - -
715A THR* 2.7 46.9 + - + +
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Residues in contact with ASN 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A THR* 3.0 29.3 + - - +
711A ASN* 1.3 76.9 - - - +
713A GLN* 1.3 67.2 + - + +
715A THR* 3.3 5.9 + - - -
716A GLU* 3.0 27.9 + - - +
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Residues in contact with GLN 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A VAL* 5.2 2.4 - - - +
653A THR* 3.6 17.2 - - + +
654A SER* 5.8 0.3 + - - -
657A ARG* 4.0 32.5 - - - +
709A THR* 2.8 36.8 + - - +
710A GLN* 3.5 28.3 + - - +
712A ASN* 1.3 78.8 - - + +
714A TRP* 1.3 56.3 + - - +
716A GLU* 3.6 2.5 - - - +
717A VAL* 3.0 33.3 + - - +
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Residues in contact with TRP 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ILE* 4.6 4.7 - - + -
653A THR* 3.5 29.4 - - + +
656A LEU* 3.6 29.8 - - + -
693A LEU* 4.3 5.2 - - - -
696A GLY* 3.7 29.4 - - - -
700A GLN* 3.4 43.9 - - + +
710A GLN* 2.7 26.3 + - - +
711A ASN* 4.1 3.6 - - - +
713A GLN* 1.3 72.0 - - - +
715A THR* 1.3 64.3 + - + +
717A VAL* 3.1 6.8 + - + +
718A MET* 2.8 59.9 + - + +
746A LEU* 4.1 9.3 - - + +
750A TYR* 3.1 27.4 + - - -
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Residues in contact with THR 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711A ASN* 2.7 29.2 + - + +
712A ASN* 3.3 8.7 + - - -
714A TRP* 1.3 79.5 - - + +
716A GLU* 1.3 59.9 + - - +
718A MET* 4.2 6.5 - - - -
719A PHE* 2.8 49.4 + - + -
750A TYR* 4.0 21.1 - - + +
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Residues in contact with GLU 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A ARG* 3.2 27.2 + - - -
662A LEU* 4.3 26.6 - - + +
712A ASN 3.0 20.0 + - - +
713A GLN* 3.6 2.1 - - - +
715A THR* 1.3 78.2 + - - +
717A VAL* 1.3 56.8 + - - +
719A PHE* 3.3 4.6 + - - +
720A MET* 2.8 33.2 + - + +
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Residues in contact with VAL 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A THR* 4.4 6.5 - - + -
656A LEU* 3.4 38.1 - - + -
657A ARG* 4.1 27.4 - - + +
660A MET* 3.4 22.1 - - + +
662A LEU* 4.1 13.5 - - + -
693A LEU* 5.0 0.9 - - + -
713A GLN* 3.0 20.9 + - - +
714A TRP* 3.1 11.8 + - + +
716A GLU* 1.3 76.3 - - + +
718A MET* 1.3 57.6 + - - +
720A MET* 3.9 1.1 - - - -
721A ALA* 3.1 25.3 + - - +
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Residues in contact with MET 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A LEU* 3.8 17.5 - - + -
714A TRP* 2.8 63.6 + - + +
715A THR 3.7 4.5 - - - +
716A GLU 3.1 0.2 - - - -
717A VAL* 1.3 77.8 - - - +
719A PHE* 1.3 59.1 + - - +
720A MET 3.2 0.2 - - - -
721A ALA* 3.7 2.0 - - + +
722A THR* 3.0 36.8 + - + +
746A LEU* 3.5 31.9 - - + -
747A PHE* 4.2 17.9 - - + -
750A TYR* 3.8 33.4 - - + +
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Residues in contact with PHE 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A THR* 2.8 36.9 + - + +
716A GLU* 3.9 5.2 - - - +
718A MET* 1.3 75.1 - - - +
720A MET* 1.3 58.4 + - - +
722A THR* 3.5 6.8 + - - -
723A ARG* 2.9 30.9 + - - +
750A TYR* 3.7 46.0 - + + -
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Residues in contact with MET 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A MET* 3.5 30.3 - - + -
662A LEU* 4.7 9.2 - - + -
674A PRO* 4.4 31.6 - - - +
675A HIS* 5.9 0.2 - - - -
676A LEU* 4.5 8.0 - - + +
716A GLU* 2.8 19.8 + - + +
717A VAL* 4.4 0.7 - - - -
719A PHE* 1.3 75.7 - - - +
721A ALA* 1.3 58.9 + - - +
723A ARG* 3.7 31.4 - - - +
724A GLU* 3.0 54.1 + - + +
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Residues in contact with ALA 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A MET* 3.6 17.9 - - + -
676A LEU* 5.3 2.8 - - - +
689A LEU* 5.4 2.2 - - + -
693A LEU* 4.0 27.8 - - + -
717A VAL 3.1 21.5 + - - +
718A MET* 3.7 9.2 - - + +
719A PHE 3.4 0.2 - - - -
720A MET* 1.3 74.7 - - - +
722A THR* 1.3 60.1 + - - +
724A GLU* 4.0 1.8 - - - +
725A LEU* 2.9 39.0 + - + +
747A PHE* 4.9 0.4 - - + -
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Residues in contact with THR 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A MET* 3.0 20.1 + - + +
719A PHE* 3.5 11.6 + - - -
721A ALA* 1.3 74.4 - - - +
723A ARG* 1.3 71.9 + - - +
725A LEU* 3.3 7.0 + - - +
726A LEU* 2.9 34.4 + - - +
747A PHE* 3.3 31.2 - - + -
750A TYR* 4.3 14.6 + - + +
751A VAL* 3.8 30.7 - - + +
759A LEU* 5.0 1.3 - - + -
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Residues in contact with ARG 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A PHE 2.9 19.2 + - - +
720A MET* 3.7 27.3 - - + +
722A THR* 1.3 80.3 + - - +
724A GLU* 1.3 67.6 + - - +
726A LEU* 3.1 10.4 + - - +
727A ARG* 3.0 31.4 + - + +
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Residues in contact with GLU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A PRO 5.4 2.1 - - - +
675A HIS* 4.4 15.0 + - - -
676A LEU* 3.4 41.1 - - + +
677A THR* 4.3 12.6 + - - +
680A LEU* 3.8 4.5 - - + +
720A MET* 3.0 39.5 + - - +
721A ALA 4.2 0.9 - - - +
723A ARG* 1.3 87.0 + - - +
725A LEU* 1.3 62.0 + - - +
727A ARG* 3.4 28.5 - - - +
728A ILE* 3.2 25.7 + - + +
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A LEU* 6.0 0.2 - - + -
680A LEU* 3.9 28.0 - - + -
686A LEU* 4.8 3.1 - - + -
689A LEU* 4.7 8.3 - - + -
690A LEU* 5.2 3.1 - - + -
693A LEU* 4.5 9.6 - - + -
721A ALA* 2.9 25.6 + - + +
722A THR* 3.6 4.9 - - - +
723A ARG 3.2 0.2 - - - -
724A GLU* 1.3 78.1 - - - +
726A LEU* 1.3 58.9 + - - +
728A ILE* 3.2 19.8 - - - +
733A LEU* 5.0 4.5 - - + -
747A PHE* 3.5 37.7 - - + -
759A LEU* 3.9 15.0 - - + -
762A LYS* 3.4 15.0 - - + +
763A LEU* 4.5 25.1 - - + -
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Residues in contact with LEU 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A THR* 2.9 29.1 + - - +
723A ARG* 3.6 6.3 - - - +
725A LEU* 1.3 75.5 - - - +
727A ARG* 1.3 64.6 + - - +
728A ILE 3.4 4.6 + - - +
751A VAL* 5.0 6.3 - - + -
755A LYS* 3.5 48.2 - - + +
758A LEU* 5.1 11.4 - - + -
759A LEU* 3.4 39.0 - - + +
762A LYS* 4.1 9.9 - - + +
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Residues in contact with ARG 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A ARG* 3.0 22.2 + - + +
724A GLU* 3.3 30.7 + - - +
726A LEU* 1.3 77.1 - - - +
728A ILE* 1.3 64.4 + - - +
729A PRO* 3.5 7.3 - - - +
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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
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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