Contacts of the helix formed by residues 710 - 729 (chain A) in PDB entry 1XR2
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 710 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PRO* 4.3 1.1 - - - -
709A ARG* 1.3 84.9 - - - +
711A TRP* 1.3 65.6 + - - +
712A ASP* 3.7 17.0 + - - +
713A GLU* 2.9 44.1 + - + +
714A VAL* 3.0 15.2 + - - +
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Residues in contact with TRP 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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412A PHE* 3.6 38.6 - + + -
413A PRO* 3.8 44.1 + - + +
415A THR* 3.6 31.6 - - + +
446A ALA* 5.8 3.6 - - + -
449A LEU* 3.5 32.1 - - + -
463A PHE* 4.3 11.0 - + - -
709A ARG 4.3 0.6 + - - -
710A ASN* 1.3 72.5 - - - +
712A ASP* 1.3 58.0 + - - +
714A VAL* 3.8 14.7 - - + +
715A ILE* 3.0 34.5 + - + +
718A LEU* 5.9 0.7 - - + -
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Residues in contact with ASP 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A VAL* 5.0 0.5 - - - +
710A ASN* 3.7 15.7 + - - +
711A TRP* 1.3 77.8 + - - +
713A GLU* 1.3 71.0 + - - +
715A ILE* 5.0 1.8 - - - -
716A PRO* 3.2 21.3 - - - +
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP* 4.3 2.5 - - + -
674A PRO* 3.2 40.6 - - - +
676A VAL* 3.8 6.3 - - + +
709A ARG* 3.1 35.5 + - + +
710A ASN* 2.9 36.7 + - + +
712A ASP* 1.3 91.6 - - - +
714A VAL* 1.3 63.7 + - - +
716A PRO* 3.5 9.8 - - - +
717A SER* 2.9 25.5 + - - -
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Residues in contact with VAL 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PHE* 5.2 2.7 - - + -
413A PRO* 3.8 20.2 - - + -
669A TRP* 4.0 8.7 - - + -
706A LEU* 3.7 28.9 - - + -
709A ARG* 3.9 7.2 - - + -
710A ASN 3.2 15.0 - - - +
711A TRP* 3.8 20.6 - - + +
713A GLU* 1.3 76.4 - - - +
715A ILE* 1.3 68.5 + - - +
717A SER* 2.9 3.3 + - - -
718A LEU* 2.8 53.9 + - + +
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Residues in contact with ILE 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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449A LEU* 5.4 12.1 - - + -
453A ILE* 3.6 21.8 - - + +
711A TRP* 3.0 14.8 + - + +
712A ASP* 5.0 1.3 - - - -
714A VAL* 1.3 80.7 - - - +
716A PRO* 1.3 70.2 - - + +
718A LEU 3.3 0.5 + - - -
719A ARG* 3.0 23.0 + - - +
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Residues in contact with PRO 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A VAL* 3.6 21.1 - - + -
712A ASP* 3.2 26.5 - - - +
713A GLU 3.5 8.1 - - - +
714A VAL 3.6 0.7 - - - -
715A ILE* 1.3 95.2 - - + +
717A SER* 1.3 57.1 + - - +
719A ARG* 3.1 32.1 + - - +
720A ASN* 2.6 37.6 + - - +
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Residues in contact with SER 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP* 3.5 34.1 + - - -
674A PRO 5.6 0.2 + - - -
676A VAL* 3.3 23.6 - - - +
677A PRO* 3.3 14.5 - - - +
682A MET* 4.0 5.2 - - - +
713A GLU 2.9 19.9 + - - -
714A VAL 2.9 4.8 + - - -
716A PRO* 1.3 79.6 - - - +
718A LEU* 1.3 59.3 + - - +
720A ASN* 3.3 6.0 + - - +
721A MET* 3.0 27.1 + - - +
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Residues in contact with LEU 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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408A THR* 4.3 19.7 - - + -
412A PHE* 4.5 10.8 - - + -
449A LEU* 5.8 5.2 - - + -
450A GLN* 6.0 1.1 - - + -
453A ILE* 3.7 23.6 - - + -
455A LEU* 4.3 27.1 - - + -
669A TRP* 3.2 35.0 - - + -
702A PRO* 5.0 0.4 - - + -
706A LEU* 5.5 1.3 - - + -
711A TRP* 5.9 0.2 - - + -
714A VAL* 2.8 34.5 + - + +
715A ILE 3.7 3.6 - - - +
717A SER* 1.3 69.5 - - - +
719A ARG* 1.3 60.5 + - - +
721A MET* 3.2 14.5 + - + +
722A VAL* 2.9 33.6 + - - +
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Residues in contact with ARG 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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453A ILE* 3.6 20.8 - - + +
715A ILE 3.0 13.5 + - - +
716A PRO* 3.3 36.3 - - - +
718A LEU* 1.3 78.0 - - - +
720A ASN* 1.3 74.7 + - - +
722A VAL* 3.1 4.6 + - - +
723A ALA* 2.9 24.8 + - + +
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Residues in contact with ASN 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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676A VAL* 4.3 5.8 - - - +
677A PRO 3.4 25.8 + - - +
678A SER* 4.3 2.4 - - - +
679A ILE* 3.6 34.6 - - + +
682A MET* 4.0 8.6 - - - +
716A PRO 2.6 31.1 + - - +
717A SER* 3.6 5.6 - - - +
719A ARG* 1.3 91.7 + - - +
721A MET* 1.3 61.6 + - - +
723A ALA* 3.6 4.5 + - - +
724A LEU* 3.2 23.7 + - - +
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Residues in contact with MET 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A THR* 4.3 4.8 - - + +
407A THR 3.3 25.1 - - - +
455A LEU* 3.8 24.0 - - + -
668A VAL* 4.4 3.4 - - - -
669A TRP* 5.0 1.6 - - - -
682A MET* 3.8 19.7 - - + -
700A ILE* 3.4 27.6 - - + +
701A ASN* 3.4 31.9 - - - +
702A PRO* 3.7 10.5 - - + -
717A SER 3.0 13.8 + - - +
718A LEU* 3.3 23.6 - - + +
720A ASN* 1.3 75.5 - - - +
722A VAL* 1.3 64.5 + - - +
724A LEU* 3.5 5.5 + - - +
725A ALA* 3.1 20.6 + - - +
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Residues in contact with VAL 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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406A THR* 4.3 6.5 - - + +
453A ILE* 3.4 35.0 - - + +
454A GLY* 3.5 26.2 - - - +
455A LEU* 3.8 18.6 - - + -
718A LEU 2.9 19.0 + - - +
719A ARG 3.6 6.5 - - - +
721A MET* 1.3 74.3 - - - +
723A ALA* 1.3 64.9 + - - +
725A ALA* 3.1 21.8 - - + +
726A LYS* 3.2 30.0 + - + +
729A ARG* 6.3 0.2 - - - +
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Residues in contact with ALA 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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679A ILE* 3.9 20.9 - - + -
719A ARG* 2.9 18.4 + - + +
720A ASN* 3.7 5.8 - - - +
722A VAL* 1.3 74.8 - - - +
724A LEU* 1.3 65.8 + - - +
726A LYS* 3.0 22.8 + - - +
727A GLU* 3.0 13.5 + - - +
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Residues in contact with LEU 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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679A ILE* 3.5 31.8 - - + +
682A MET* 4.3 9.2 - - + -
683A ARG* 3.8 25.4 - - + +
686A VAL* 4.1 20.9 - - + -
700A ILE* 4.6 11.9 - - + -
720A ASN 3.2 12.0 + - - +
721A MET* 3.7 7.2 - - - +
723A ALA* 1.3 79.1 - - - +
725A ALA* 1.3 68.0 + - - +
727A GLU* 4.3 8.5 - - + -
728A MET* 2.9 49.4 + - + +
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Residues in contact with ALA 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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404A PHE* 3.9 16.6 - - - +
406A THR* 3.4 31.2 - - + -
700A ILE* 4.9 3.8 - - + -
721A MET 3.1 8.0 + - - +
722A VAL* 3.1 12.3 - - + +
723A ALA 3.1 1.0 - - - -
724A LEU* 1.3 84.6 - - - +
726A LYS* 1.3 61.9 + - - +
728A MET* 3.2 17.5 + - - +
729A ARG* 3.3 23.7 + - - +
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Residues in contact with LYS 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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453A ILE 5.4 2.0 + - - -
454A GLY* 5.7 3.5 - - - -
722A VAL* 3.6 30.1 - - + +
723A ALA* 3.0 11.5 + - - +
725A ALA* 1.3 74.3 - - - +
727A GLU* 1.3 66.0 + - - +
729A ARG* 2.9 47.5 + - - +
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Residues in contact with GLU 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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679A ILE* 5.6 3.4 - - + -
723A ALA 3.0 12.4 + - - +
724A LEU* 3.3 18.6 + - + +
726A LYS* 1.3 76.1 - - - +
728A MET* 1.3 65.9 + - + +
729A ARG 3.2 8.1 + - - +
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Residues in contact with MET 728 (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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403A LEU* 5.3 0.5 - - - +
404A PHE* 3.4 39.7 - - + -
683A ARG* 5.0 10.8 - - + +
686A VAL* 4.1 26.7 - - + -
687A GLU* 5.5 6.3 - - + +
690A LEU* 5.2 5.6 - - + -
700A ILE* 5.9 0.9 - - + -
724A LEU* 2.9 45.6 + - + +
725A ALA* 3.2 14.8 - - - +
726A LYS 3.1 0.2 - - - -
727A GLU* 1.3 79.0 - - - +
729A ARG* 1.3 57.8 + - - +
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Residues in contact with ARG 729 (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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402A PRO* 3.8 19.7 - - - +
403A LEU* 2.8 39.3 + - + +
404A PHE* 3.2 24.9 + - + -
406A THR* 4.9 0.2 - - - +
456A ASP* 3.4 22.4 + - - -
722A VAL* 6.3 0.4 - - - +
725A ALA* 3.5 22.9 + - - +
726A LYS* 2.9 42.3 + - - +
727A GLU* 3.4 7.3 - - - +
728A MET* 1.3 81.2 - - - +
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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