Contacts of the helix formed by residues 706 - 723 (chain A) in PDB entry 1W6J
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 SER 706 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 2.7 34.5 + - - -
94A TRP* 4.7 0.5 - - - +
95A THR 4.0 16.5 + - - -
388A ASP* 4.1 19.8 + - - +
704A TYR 3.4 0.8 - - - -
705A THR* 1.3 76.7 - - - +
707A TYR* 1.3 61.3 + - - +
708A ARG 3.1 3.6 - - - -
709A ASN* 3.0 11.3 + - - +
710A ILE* 2.8 41.3 + - - +
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Residues in contact with TYR 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TRP* 2.9 42.2 + + - -
388A ASP* 4.6 6.7 - - - -
391A PHE* 4.0 10.1 - + - -
581A TRP 5.4 1.6 + - - -
587A TYR* 4.2 10.3 + + - -
649A ILE* 4.8 2.0 - - - +
650A HIS* 4.7 11.4 - - + +
654A TRP* 3.6 33.0 - + - -
693A ALA* 4.0 14.1 - - + -
704A TYR* 3.2 53.7 + + + +
706A SER* 1.3 78.4 - - - +
708A ARG* 1.3 57.9 + - - +
710A ILE* 4.5 3.8 - - + -
711A PHE* 3.1 54.9 + + + +
712A PRO* 3.4 4.3 - - - +
1733A R71 4.8 0.2 - - - +
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Residues in contact with ARG 708 (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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54A TYR* 3.1 28.6 + - - -
373A LEU* 6.2 1.2 - - - +
649A ILE* 4.2 14.5 - - + +
650A HIS* 6.1 0.4 - - - +
686A ASP* 4.6 3.8 + - - -
687A TRP* 3.3 41.7 + - + +
688A PRO 3.6 22.4 - - - +
689A GLN* 3.4 44.4 + - - +
704A TYR 4.6 1.8 + - - -
705A THR* 3.2 39.5 + - - +
707A TYR* 1.3 78.2 - - - +
709A ASN* 1.3 64.2 + - - +
712A PRO* 3.2 18.7 - - - +
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Residues in contact with ASN 709 (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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54A TYR* 4.2 12.1 + - - -
80A GLY 5.3 0.7 - - - +
83A PHE* 3.9 13.9 - - - -
84A TYR* 3.4 41.6 - - + +
87A LEU* 4.9 0.6 - - - +
685A GLY 4.9 0.2 - - - +
686A ASP* 3.0 25.3 + - - +
687A TRP* 4.0 13.7 + - + -
705A THR* 4.2 5.7 + - - +
706A SER* 3.0 6.9 + - - +
708A ARG* 1.3 90.0 - - - +
710A ILE* 1.3 67.0 + - - +
711A PHE 3.4 1.3 + - - -
712A PRO* 3.4 2.3 - - - +
713A ILE* 3.2 30.5 + - + +
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Residues in contact with ILE 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.5 32.3 - - + +
388A ASP* 3.4 29.8 - - - +
391A PHE* 4.0 32.8 - - + +
392A ALA* 3.9 9.4 - - - +
395A ALA* 3.4 12.0 - - + +
706A SER* 2.8 32.1 + - - +
707A TYR* 4.5 4.3 - - + -
709A ASN* 1.3 75.1 - - - +
711A PHE* 1.3 67.9 + - + +
713A ILE* 3.4 4.1 + - - +
714A TRP* 3.0 36.0 + - + +
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Residues in contact with PHE 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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391A PHE* 3.9 22.0 - + - -
587A TYR* 5.7 0.4 - + - -
590A TRP* 3.5 28.3 - + - -
650A HIS* 5.3 4.9 - - + -
653A CYS* 3.4 16.9 - - + +
654A TRP* 3.5 29.2 - + - +
657A MET* 3.8 17.5 - - - -
707A TYR* 3.1 57.1 + + + +
710A ILE* 1.3 76.5 - - + +
712A PRO* 1.3 65.2 - - + +
714A TRP* 3.5 24.5 - + - +
715A ALA* 2.8 32.4 + - - +
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Residues in contact with PRO 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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649A ILE* 3.4 22.4 - - + -
653A CYS* 3.4 10.7 - - - -
677A LEU* 4.4 9.2 - - + -
687A TRP* 3.6 33.9 - - + +
707A TYR 3.4 7.2 - - - +
708A ARG 3.2 22.9 - - - +
709A ASN 3.4 7.9 - - - +
711A PHE* 1.3 87.8 - - + +
713A ILE* 1.3 64.2 + - - +
716A LEU* 2.9 34.2 + - + +
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Residues in contact with ILE 713 (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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77A ALA* 4.2 11.1 - - - +
80A GLY* 3.5 42.0 - - - +
81A MET* 3.6 27.8 - - + +
84A TYR* 4.1 14.1 - - + -
395A ALA* 3.5 25.4 - - + +
396A LEU* 4.3 7.2 - - + -
399A ALA* 3.8 9.2 - - + +
687A TRP* 4.3 3.1 - - + -
709A ASN* 3.2 24.6 + - + +
710A ILE* 3.6 5.4 - - - +
712A PRO* 1.3 76.4 - - - +
714A TRP* 1.3 57.9 - - - +
717A GLY* 2.9 28.8 + - - -
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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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391A PHE* 3.7 38.6 - + - -
394A GLN* 3.5 40.2 + - + +
395A ALA* 3.7 17.9 - - + +
398A GLU* 2.9 42.0 + - + +
462A LYS* 4.9 4.5 - - - -
590A TRP* 4.5 10.3 - + - -
657A MET* 3.6 22.7 - - + -
710A ILE* 3.0 24.4 + - + +
711A PHE* 3.5 33.0 - + - +
713A ILE* 1.3 77.4 - - - +
715A ALA* 1.3 57.3 + - - +
717A GLY* 3.8 0.3 - - - -
718A ARG* 2.9 33.1 + - - +
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Residues in contact with ALA 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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653A CYS* 4.1 20.6 - - + +
656A MET* 4.4 9.3 - - + +
657A MET* 3.8 24.8 - - + -
660A MET* 3.6 8.8 - - + +
677A LEU* 4.4 8.1 - - + -
711A PHE 2.8 20.3 + - - +
712A PRO 4.2 1.1 - - - +
714A TRP* 1.3 71.9 - - - +
716A LEU* 1.3 61.9 + - - +
718A ARG* 3.5 1.9 + - - -
719A PHE* 3.0 28.1 + - - +
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Residues in contact with LEU 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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73A ALA* 3.5 25.4 - - - +
76A GLY 3.9 3.6 - - - -
77A ALA* 3.9 20.0 - - + +
674A VAL* 3.9 38.4 - - + +
677A LEU* 4.1 24.5 - - + -
678A LEU* 4.0 13.7 - - + -
687A TRP* 3.8 26.5 - - + -
712A PRO 2.9 24.7 + - - +
715A ALA* 1.3 76.4 - - - +
717A GLY* 1.3 58.4 + - - +
719A PHE* 3.4 1.9 + - - +
720A SER* 3.0 30.3 + - - -
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Residues in contact with GLY 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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77A ALA* 4.1 4.2 - - - +
398A GLU 3.4 23.2 - - - +
399A ALA* 3.8 13.5 - - - -
713A ILE 2.9 18.6 + - - -
714A TRP 3.9 0.2 - - - -
716A LEU* 1.3 75.7 - - - +
718A ARG* 1.3 65.5 + - - +
720A SER* 3.1 8.8 + - - -
721A GLN* 2.9 20.8 + - - +
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Residues in contact with ARG 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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398A GLU* 2.8 46.0 + - - +
594A GLU* 2.7 33.3 + - - -
657A MET* 3.0 36.5 + - + +
660A MET* 3.8 31.2 - - + -
661A ALA* 3.9 8.8 - - - +
663A ARG* 5.5 2.0 - - - +
714A TRP* 2.9 28.1 + - - +
715A ALA* 3.7 5.2 - - - +
717A GLY* 1.3 74.8 - - - +
719A PHE* 1.3 63.3 + - - +
721A GLN* 3.3 6.0 + - + +
722A LEU* 3.0 34.1 + - + +
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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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73A ALA* 3.8 14.8 - - + -
660A MET* 3.6 17.9 - - + -
667A ILE* 4.4 3.1 - - + -
670A GLN* 4.4 6.1 - - + -
671A GLU* 3.5 44.2 - - + -
674A VAL* 3.6 27.4 - - + -
715A ALA 3.0 18.1 + - - +
716A LEU 3.7 3.8 - - - +
717A GLY 3.3 0.2 - - - -
718A ARG* 1.3 75.0 - - - +
720A SER* 1.3 65.8 + - - +
722A LEU 3.2 1.4 + - - -
723A TYR* 3.1 58.7 + + + +
726A ARG* 4.5 2.9 - - + -
728A LEU* 4.1 6.1 - - + -
729A ALA* 3.8 30.5 - - + -
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Residues in contact with SER 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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73A ALA* 4.0 5.2 - - - -
74A PHE* 4.1 8.7 - - - -
77A ALA* 5.8 0.2 - - - +
398A GLU 5.4 0.2 + - - -
399A ALA* 5.6 2.4 + - - -
716A LEU 3.0 15.4 + - - -
717A GLY* 3.1 12.6 + - - -
719A PHE* 1.3 78.9 - - - +
721A GLN* 1.3 63.8 + - - +
724A PRO 3.8 8.5 - - - -
729A ALA* 3.7 17.5 - - - -
732A PRO* 3.2 53.9 - - - +
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Residues in contact with GLN 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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397A LEU 4.7 1.9 - - - +
398A GLU* 3.2 40.8 - - - +
399A ALA 6.0 0.4 - - - -
400A GLY* 5.9 1.1 - - - +
470A LYS* 5.3 8.3 - - - +
717A GLY 2.9 17.5 + - - +
718A ARG* 3.6 5.8 - - - +
719A PHE 3.2 0.2 - - - -
720A SER* 1.3 80.0 + - - +
722A LEU* 1.3 65.0 + - + +
724A PRO* 3.4 12.5 - - - +
732A PRO* 4.6 8.2 - - - +
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Residues in contact with LEU 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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660A MET* 3.7 47.3 - - + +
663A ARG* 3.6 37.2 - - - +
718A ARG* 3.0 26.3 + - + +
721A GLN* 1.3 80.9 - - + +
723A TYR* 1.3 88.6 + - + +
724A PRO* 3.3 6.3 - - - +
725A GLU* 4.4 1.0 - - - +
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Residues in contact with TYR 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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660A MET* 4.5 2.9 - - - +
663A ARG* 5.2 6.9 - - - -
664A HIS 4.3 2.9 + - - -
667A ILE* 3.7 34.4 - - + +
670A GLN* 2.6 38.2 + - - -
719A PHE* 3.1 45.9 + + + +
720A SER 4.2 0.7 - - - -
722A LEU* 1.3 110.1 - - + +
724A PRO* 1.3 57.3 - - - +
725A GLU* 3.0 18.4 - - - -
726A ARG* 2.9 37.2 + - + -
729A ALA* 3.1 15.9 - - - +
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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
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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