Contacts of the helix formed by residues 632 - 650 (chain A) in PDB entry 5LUQ
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 GLU 632 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A CYS* 2.6 9.4 + - + -
631A ARG* 1.3 74.9 - - + +
633A ILE* 1.3 65.5 + - + +
634A LEU 3.3 1.6 - - - -
635A PRO* 3.0 17.8 - - - +
636A GLU* 4.2 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PHE* 3.6 30.5 - - + -
628A GLU* 3.4 49.1 - - + +
629A PHE 4.1 0.2 - - - +
630A CYS* 2.7 47.1 + - + +
632A GLU* 1.3 77.5 - - + +
634A LEU* 1.3 55.2 + - + +
635A PRO* 3.3 2.0 - - - -
636A GLU* 3.6 7.6 + - + +
637A LYS* 2.9 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU 4.1 0.9 - - - +
629A PHE* 3.4 55.4 - - + +
630A CYS 3.0 16.9 + - - +
631A ARG* 4.7 6.5 - - - +
632A GLU 4.1 0.2 - - - +
633A ILE* 1.3 78.0 - - - +
635A PRO* 1.4 61.8 - - - +
637A LYS* 3.9 13.9 - - + -
638A GLN* 3.2 8.6 - - - +
666A PHE 4.7 0.2 - - - +
667A TYR* 3.5 27.1 - - + -
668A LYS* 3.5 38.1 - - + +
669A LEU* 3.0 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ARG 3.9 11.7 - - - +
632A GLU* 3.0 23.1 - - - +
634A LEU* 1.4 91.1 - - - +
636A GLU* 1.3 72.0 + - + +
637A LYS 3.2 1.1 - - - -
638A GLN* 3.2 12.0 + - - +
639A ALA* 3.0 26.5 + - - +
669A LEU* 4.2 11.7 - - + -
672A ILE* 5.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PHE* 5.9 2.6 - - - -
632A GLU 4.2 16.1 - - - +
633A ILE* 4.1 9.0 - - + +
635A PRO* 1.3 78.1 - - + +
637A LYS* 1.3 66.2 + - - +
639A ALA* 4.7 4.0 - - - -
640A GLU* 3.0 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PHE* 6.0 2.9 - - - -
553A VAL* 3.8 27.0 - - - +
554A ASN* 3.9 13.9 + - - +
624A ILE* 4.9 11.7 - - + -
628A GLU 4.9 2.2 - - - +
629A PHE* 5.4 0.2 - - + -
633A ILE* 2.9 46.3 + - + +
634A LEU* 3.9 9.0 - - + -
636A GLU* 1.3 75.2 - - - +
638A GLN* 1.3 57.6 + - - +
640A GLU* 4.6 8.9 + - - -
641A PHE* 2.8 53.2 + - - +
667A TYR* 3.5 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LEU 3.2 19.2 + - - +
635A PRO* 3.2 9.6 + - - +
637A LYS* 1.3 75.7 - - - +
639A ALA* 1.3 68.8 + - - +
642A PHE* 3.0 37.2 + - + +
663A ILE* 6.0 0.4 - - - -
664A SER* 4.5 5.6 + - - +
667A TYR* 3.3 41.5 + - + +
669A LEU* 3.2 37.8 + - - +
673A THR* 3.6 18.8 - - + +
704A PHE* 6.1 1.2 - - + -
707A PHE* 4.8 17.3 - - + -
740A ILE* 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A PRO 3.0 14.9 + - - +
636A GLU* 4.3 4.0 - - - +
638A GLN* 1.3 79.1 - - - +
640A GLU* 1.3 65.9 + - + +
643A GLU* 3.7 10.9 - - - +
700A LYS* 5.7 8.1 - - + +
703A CYS* 3.1 40.8 - - + +
704A PHE* 6.4 1.8 - - + -
707A PHE* 5.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASN* 4.5 16.5 + - - +
636A GLU* 3.0 41.6 + - - +
637A LYS* 4.4 11.1 + - - -
639A ALA* 1.3 75.7 - - + +
641A PHE* 1.3 58.1 + - + +
642A PHE 2.9 13.6 + - - -
643A GLU* 3.2 16.5 + - - +
644A PRO* 3.3 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A VAL* 5.5 1.6 - - + -
554A ASN* 5.4 2.5 - - - +
557A SER* 4.3 16.8 - - - -
620A PHE* 4.4 15.0 - + - -
624A ILE* 5.3 5.6 - - + -
637A LYS* 2.8 42.1 + - + +
640A GLU* 1.3 76.7 - - + +
642A PHE* 1.3 64.1 + - - +
644A PRO* 3.3 8.3 - - - +
645A TRP* 2.9 57.8 - + + +
659A ARG* 4.7 2.7 - - + -
660A LEU* 5.4 1.1 - - + -
663A ILE* 3.4 52.3 - - + -
667A TYR* 3.8 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLN* 3.0 24.3 + - + +
639A ALA* 4.6 2.7 - - - +
640A GLU 2.9 1.2 + - - -
641A PHE* 1.3 84.7 - - - +
643A GLU* 1.3 67.7 + - + +
645A TRP* 3.3 9.9 + - - +
646A VAL* 3.4 24.1 + - + +
660A LEU* 5.8 4.5 - - + -
663A ILE* 5.1 5.4 - - + +
664A SER* 4.0 27.1 - - - -
703A CYS* 4.4 4.3 - - + -
706A LEU* 4.6 3.1 - - + -
707A PHE* 3.4 53.4 - + + -
710A PHE* 3.2 41.3 - + - -
737A PRO* 5.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ALA 3.7 15.9 - - - +
640A GLU* 3.2 3.3 + - - +
642A PHE* 1.3 75.8 - - + +
644A PRO* 1.3 71.9 - - + +
646A VAL* 4.3 1.6 - - - +
647A TYR* 3.1 24.0 + - - +
702A SER* 4.2 6.1 + - - -
703A CYS* 3.2 31.6 + - - -
706A LEU* 3.6 30.3 - - + +
710A PHE* 5.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A ASN* 5.0 14.4 - - - +
640A GLU 3.3 11.9 - - - +
641A PHE* 3.3 14.8 - - - +
643A GLU* 1.3 95.0 - - + +
645A TRP* 1.3 63.8 + - + +
647A TYR* 3.3 10.4 - - + +
648A SER* 2.8 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A SER* 5.0 4.8 + - - -
560A LEU* 3.8 31.4 - - + -
561A ASN* 5.2 6.5 + - - -
564A LEU* 5.7 2.2 - - + -
617A PRO* 4.5 11.7 - - + -
620A PHE* 4.2 15.5 - + - -
641A PHE* 2.9 59.4 - + + +
642A PHE* 3.6 7.6 - - - +
643A GLU 3.3 0.2 - - - -
644A PRO* 1.3 81.8 - - + +
646A VAL* 1.3 67.9 + - - +
648A SER* 2.6 30.3 + - - -
649A PHE* 2.9 7.7 + - + +
656A GLN* 3.7 28.7 - - + -
659A ARG* 3.9 21.8 - - + -
660A LEU* 3.1 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A PHE* 3.4 26.3 + - + +
643A GLU 4.4 0.2 - - - +
645A TRP* 1.3 70.3 - - - +
647A TYR* 1.3 70.4 + - - +
649A PHE* 2.9 23.3 + - + +
650A SER* 3.1 9.2 + - - -
660A LEU* 3.4 28.0 - - + -
710A PHE* 3.4 60.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A TYR* 6.5 0.7 - + - -
643A GLU 3.1 21.7 + - - +
644A PRO* 3.3 11.0 - - + +
646A VAL* 1.3 75.6 - - - +
648A SER* 1.3 60.9 + - - +
650A SER* 2.5 49.3 + - - -
651A TYR* 5.4 12.0 + + - -
710A PHE* 5.1 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A ASN* 5.7 6.1 - - - -
564A LEU* 4.9 12.6 - - - +
644A PRO 2.8 18.2 + - - -
645A TRP* 2.6 27.5 + - - -
647A TYR* 1.3 79.6 - - - +
649A PHE* 1.3 59.8 + - - +
650A SER* 3.3 0.4 - - - -
651A TYR* 4.1 17.4 + - - -
656A GLN* 3.1 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TRP* 2.9 9.1 + - + +
646A VAL* 2.9 25.3 + - + +
648A SER* 1.3 74.9 + - - +
650A SER* 1.3 51.3 + - - +
651A TYR 2.3 22.6 + - - -
652A GLU* 2.4 52.3 + - - +
653A LEU 3.1 47.6 - - - -
656A GLN* 4.0 13.2 - - + +
657A SER* 4.2 15.0 - - - +
660A LEU* 4.8 8.1 - - + -
713A GLU 6.4 0.2 - - - -
714A VAL* 5.3 13.9 - - + -
717A LYS* 5.0 4.5 - - + -
730A LEU* 3.8 25.6 - - + -
734A LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A VAL 3.1 6.1 + - - -
647A TYR* 2.5 42.0 + - - -
648A SER 4.7 0.3 - - - -
649A PHE* 1.3 68.7 - - - +
651A TYR* 1.3 74.0 + - - +
652A GLU* 3.5 7.1 - - - +
713A GLU* 5.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
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