Contacts of the helix formed by residues 705 - 722 (chain A) in PDB entry 5KMO
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 THR 705 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A VAL* 3.7 19.7 - - + +
697A GLU* 4.4 6.9 + - - -
703A LYS* 5.5 3.7 - - + +
704A PHE* 1.3 79.6 - - - +
706A THR* 1.3 65.8 + - - +
707A GLU* 3.4 25.2 + - - +
708A SER* 2.7 31.6 + - - -
709A ASP* 3.2 5.2 + - - +
768A PRO* 5.6 0.3 - - - +
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Residues in contact with THR 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ALA* 3.7 37.7 + - + +
645A HIS* 5.0 9.2 + - - -
646A PHE 5.0 2.4 + - - +
647A VAL* 3.7 12.6 - - - +
705A THR* 1.3 73.5 - - - +
707A GLU* 1.4 71.2 + - - +
709A ASP* 3.0 34.2 + - + +
710A VAL* 3.3 14.0 + - + +
774A ILE* 5.3 2.0 - - + -
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Residues in contact with GLU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A THR* 3.4 23.9 + - - +
706A THR* 1.4 89.9 + - - +
708A SER* 1.3 54.3 + - - +
710A VAL* 3.3 24.5 - - - +
711A TRP 3.7 0.2 + - - -
768A PRO* 3.9 39.0 - - + +
769A GLN* 4.8 4.5 - - - +
771A ARG* 2.8 22.8 + - + -
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Residues in contact with SER 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A VAL* 4.7 1.9 - - - +
695A PRO* 3.5 22.6 - - - +
697A GLU* 3.9 11.4 + - - -
698A SER* 3.9 9.8 + - - -
704A PHE* 3.6 9.9 - - - +
705A THR* 2.7 35.9 + - - -
707A GLU* 1.3 74.8 - - - +
709A ASP* 1.4 63.9 + - - +
710A VAL 3.2 0.7 - - - -
711A TRP* 3.2 14.4 + - - +
712A SER* 3.3 14.8 + - - -
771A ARG* 3.7 8.7 - - - +
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Residues in contact with ASP 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A MET* 3.7 24.7 - - + +
646A PHE 3.8 4.5 - - - +
647A VAL* 3.4 13.1 - - - +
648A HIS* 3.2 33.8 + - - +
649A ARG* 3.6 12.1 + - - -
651A LEU* 3.9 8.7 - - - +
705A THR 3.2 11.0 + - - +
706A THR* 3.0 18.2 + - + +
708A SER* 1.4 79.0 + - - +
710A VAL* 1.4 56.8 + - + +
712A SER* 3.2 8.3 + - - -
713A PHE* 2.8 28.5 + - - +
774A ILE* 6.0 0.4 - - - -
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Residues in contact with VAL 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A THR* 3.3 16.4 + - + +
707A GLU* 3.3 17.3 - - - +
708A SER 3.2 0.6 - - - -
709A ASP* 1.4 74.7 - - + +
711A TRP* 1.3 59.1 - - - +
713A PHE* 3.7 6.1 - - - +
714A GLY 2.9 24.1 + - - -
763A CYS* 3.3 24.1 - - - +
771A ARG* 3.9 20.6 - - + -
772A HIS 3.8 23.6 - - - +
773A SER* 5.2 0.9 - - - -
774A ILE* 4.0 36.1 - - + +
777A VAL* 5.7 0.7 - - + -
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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
----------------------------------------------------------
692A ARG 5.2 1.6 + - - -
693A TRP 3.6 10.5 - - - -
694A MET 3.5 9.9 + - - -
695A PRO* 3.5 29.6 - - + -
696A PRO* 3.7 27.8 - - + -
707A GLU 3.7 0.8 + - - -
708A SER 3.2 11.3 + - - +
710A VAL* 1.3 82.6 - - - +
712A SER* 1.4 55.8 + - - +
714A GLY 3.2 2.4 + - - -
715A VAL* 3.0 35.3 + - + +
740A ILE* 4.5 15.8 - - + +
743A GLY* 6.5 1.1 - - - -
744A ARG 5.8 4.7 - - - -
745A GLU* 5.7 4.9 - - + -
763A CYS 3.3 13.0 - - - -
764A TRP* 3.3 58.8 + + + -
765A GLN 4.5 1.3 - - - -
766A ARG* 4.5 4.3 - - - -
771A ARG* 3.5 27.8 - - - +
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Residues in contact with SER 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ARG 5.8 2.1 + - - -
651A LEU* 4.0 26.1 + - - -
693A TRP* 2.7 29.5 + - - +
694A MET* 4.7 3.1 - - - +
695A PRO* 4.7 1.6 - - - +
708A SER 3.3 9.7 + - - -
709A ASP* 3.2 13.7 + - - -
711A TRP* 1.4 73.4 - - - +
713A PHE* 1.3 60.5 + - - +
715A VAL* 3.2 7.1 + - - +
716A VAL* 2.9 31.4 + - - +
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Residues in contact with PHE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ALA* 3.4 22.2 - - + -
634A VAL* 3.7 23.6 - - + -
635A ALA* 3.5 28.7 - - + -
638A MET* 4.4 3.1 - - + -
651A LEU* 3.8 14.5 - - + +
709A ASP 2.8 17.2 + - - +
710A VAL 3.3 4.2 + - - +
712A SER* 1.3 70.6 - - - +
714A GLY* 1.3 59.0 + - - +
716A VAL* 2.9 10.9 + - + +
717A LEU* 2.8 48.3 + - + +
720A ILE* 5.5 0.2 - - + -
763A CYS* 4.5 4.3 - - - -
774A ILE* 4.0 16.4 - - + -
777A VAL* 3.4 32.8 - - + -
781A LEU* 3.6 15.0 - - + -
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Residues in contact with GLY 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A VAL 2.9 10.9 + - - -
711A TRP 3.2 5.6 + - - -
713A PHE* 1.3 77.5 - - - +
715A VAL* 1.4 58.9 + - - +
717A LEU* 3.2 22.6 - - - +
718A TRP 3.2 5.4 + - - -
760A MET* 4.0 5.0 - - - +
763A CYS* 3.6 26.0 - - - -
764A TRP* 3.4 18.4 - - - -
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Residues in contact with VAL 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ARG 3.9 13.9 - - - +
693A TRP* 3.5 22.4 - - + +
711A TRP* 3.0 33.0 + - + +
712A SER 3.5 7.0 - - - +
713A PHE 3.2 0.2 - - - -
714A GLY* 1.4 71.3 - - - +
716A VAL* 1.4 60.8 + - - +
718A TRP* 3.3 4.8 + - - +
719A GLU* 3.0 26.1 + - - +
727A PRO* 3.5 35.2 - - + -
746A LEU* 4.4 7.2 - - + -
764A TRP* 3.8 18.4 - - + +
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Residues in contact with VAL 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A VAL* 4.3 20.6 - - + -
651A LEU* 3.9 14.1 - - + +
652A ALA* 3.7 34.3 - - - +
653A THR* 3.7 20.6 - - + +
656A CYS* 5.6 0.7 - - - -
693A TRP* 4.6 0.4 - - + -
712A SER 2.9 19.1 + - - +
713A PHE* 2.9 13.5 + - + +
715A VAL* 1.4 75.3 - - - +
717A LEU* 1.4 50.1 + - - +
719A GLU* 2.9 29.8 + - - +
720A ILE* 2.9 29.8 + - + +
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Residues in contact with LEU 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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631A ALA* 3.9 18.2 - - + -
713A PHE* 2.8 35.4 + - + +
714A GLY* 3.2 13.0 - - - +
716A VAL* 1.4 72.1 - - - +
718A TRP* 1.3 60.3 + - - +
720A ILE* 3.4 6.8 + - - +
721A PHE* 3.1 59.9 + - + -
756A VAL* 4.0 10.3 - - + +
759A ILE* 3.7 32.1 - - + -
760A MET* 3.7 26.0 - - + +
763A CYS* 5.3 0.7 - - - -
781A LEU* 4.1 7.6 - - + -
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Residues in contact with TRP 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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714A GLY 3.2 7.9 + - - +
715A VAL 3.3 8.3 + - - +
717A LEU* 1.3 73.4 - - - +
719A GLU* 1.4 59.0 + - + +
721A PHE 3.5 1.2 + - - -
722A THR* 2.7 67.9 + - + +
725A LYS* 3.4 21.3 - - + -
726A GLN 3.5 14.4 - - - -
727A PRO* 3.5 26.7 - - + -
728A TRP 4.5 1.6 - - - -
729A TYR* 5.2 8.1 - + - -
730A GLN* 6.2 0.2 - - - -
746A LEU* 3.5 35.1 - - + +
747A GLU 2.9 31.3 + - - +
749A PRO* 3.7 14.1 - - + +
760A MET* 3.8 17.4 - - - +
764A TRP* 4.1 11.2 - + + -
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Residues in contact with GLU 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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598A ASN* 3.5 12.0 + - - -
601A LEU* 4.2 1.1 - - - -
652A ALA* 3.7 1.2 - - - -
653A THR* 2.6 46.7 + - + +
654A ARG 5.0 0.7 + - - -
693A TRP* 2.7 42.9 + - - +
715A VAL 3.0 14.3 + - - +
716A VAL* 2.9 12.9 + - - +
718A TRP* 1.4 73.2 - - - +
720A ILE* 1.3 63.9 + - - +
722A THR* 3.1 8.5 + - - -
723A TYR 3.1 5.0 + - - -
724A GLY* 2.7 29.7 + - - +
725A LYS 4.0 15.7 - - - +
727A PRO* 4.2 9.4 - - + -
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Residues in contact with ILE 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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597A LEU* 4.9 0.2 - - + -
601A LEU* 3.7 18.4 - - + +
627A LEU* 3.4 52.7 - - + +
630A VAL* 4.1 18.2 - - + -
631A ALA* 3.8 31.4 - - + +
634A VAL* 4.8 4.9 - - + -
653A THR* 4.3 6.3 - - + -
713A PHE* 5.5 1.6 - - + -
716A VAL* 2.9 35.9 + - + +
717A LEU* 3.6 8.3 - - + +
719A GLU* 1.3 74.4 - - - +
721A PHE* 1.3 65.1 + - + +
723A TYR* 3.0 22.0 + - - -
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Residues in contact with PHE 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 3.9 19.5 - - + -
627A LEU* 3.8 37.7 - - + -
628A LEU* 3.9 20.6 - - + -
631A ALA* 4.8 0.7 - - + -
717A LEU* 3.1 40.5 + - + +
718A TRP 3.7 0.4 - - - -
720A ILE* 1.3 83.9 - - + +
722A THR* 1.3 57.9 + - - +
723A TYR* 3.3 6.0 + - - -
749A PRO* 3.5 29.3 - - + +
750A ARG 5.2 0.2 + - - -
751A ALA* 3.7 36.3 + - - +
752A CYS* 3.9 11.4 - - + -
753A PRO* 4.4 3.6 - - + -
756A VAL* 3.6 27.1 - - + -
760A MET* 4.2 2.5 - - + -
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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
----------------------------------------------------------
718A TRP* 2.7 62.2 + - + +
719A GLU* 3.1 8.0 + - - -
721A PHE* 1.3 75.5 - - - +
723A TYR* 1.4 70.9 + - - +
725A LYS* 3.3 44.5 + - + +
749A PRO* 3.5 23.1 - - + -
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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