Contacts of the helix formed by residues 703 - 724 (chain Q) in PDB entry 5IJO
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 PRO 703 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701Q SER 4.1 0.6 - - - -
702Q VAL* 1.3 79.5 - - - +
704Q CYS* 1.3 61.6 + - - +
705Q GLN* 3.3 7.9 - - + +
706Q LEU* 3.3 12.2 + - + +
707Q LEU* 3.0 24.7 + - - +
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Residues in contact with CYS 704 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703Q PRO* 1.3 70.5 - - - +
705Q GLN* 1.3 67.4 + - - +
707Q LEU* 3.0 9.1 + - - +
708Q GLU* 2.9 24.1 + - - +
799Q CYS* 4.3 23.8 - - + -
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Residues in contact with GLN 705 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703Q PRO* 3.3 5.8 - - + +
704Q CYS* 1.3 79.2 - - - +
706Q LEU* 1.3 56.9 + - - +
708Q GLU* 3.2 7.6 + - - +
709Q SER* 2.9 26.9 + - - -
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Residues in contact with LEU 706 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702Q VAL* 4.4 9.6 - - + -
703Q PRO* 3.3 22.4 + - + +
704Q CYS 3.1 0.4 - - - -
705Q GLN* 1.3 77.5 - - - +
707Q LEU* 1.3 64.8 + - - +
709Q SER* 3.0 8.8 + - - -
710Q VAL* 2.9 24.1 + - - +
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Residues in contact with LEU 707 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702Q VAL* 5.3 4.9 - - + +
703Q PRO 3.0 13.2 + - - +
704Q CYS* 3.0 13.1 + - - +
706Q LEU* 1.3 75.7 - - - +
708Q GLU* 1.3 58.9 + - - +
710Q VAL* 3.3 6.5 + - - +
711Q LEU* 2.9 30.3 + - - +
792Q LEU* 5.1 5.6 - - + +
795Q TRP* 5.2 15.5 - - + +
796Q LYS* 5.3 11.2 - - - +
799Q CYS* 6.0 2.9 - - + -
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Residues in contact with GLU 708 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704Q CYS 2.9 12.0 + - - +
705Q GLN* 3.5 10.3 - - - +
707Q LEU* 1.3 76.6 - - - +
709Q SER* 1.3 59.7 + - - +
711Q LEU* 3.3 6.1 + - - +
712Q GLN* 2.8 32.3 + - - +
796Q LYS* 6.2 3.1 - - - -
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Residues in contact with SER 709 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705Q GLN 2.9 13.8 + - - -
706Q LEU* 3.0 12.5 + - - -
708Q GLU* 1.3 77.5 - - - +
710Q VAL* 1.3 62.0 + - - +
712Q GLN* 3.2 5.4 + - - +
713Q GLU* 3.0 23.7 + - - +
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Residues in contact with VAL 710 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706Q LEU 2.9 15.3 + - - +
707Q LEU* 3.8 5.8 - - - +
709Q SER* 1.3 75.6 - - - +
711Q LEU* 1.3 64.1 + - - +
713Q GLU* 3.2 6.0 + - - +
714Q LEU* 2.9 27.2 + - - +
792Q LEU* 5.3 5.6 - - + -
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Residues in contact with LEU 711 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707Q LEU 2.9 18.6 + - - +
708Q GLU* 3.6 7.2 - - - +
710Q VAL* 1.3 78.5 - - - +
712Q GLN* 1.3 57.5 + - - +
714Q LEU* 3.8 4.0 - - - +
715Q LYS* 2.9 29.8 + - - +
789Q TYR* 5.9 1.8 - - - +
792Q LEU* 4.1 28.0 - - + +
793Q ALA* 5.4 2.0 - - - +
796Q LYS* 5.5 7.0 - - + -
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Residues in contact with GLN 712 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708Q GLU 2.8 17.7 + - - +
709Q SER* 3.6 5.6 - - - +
711Q LEU* 1.3 77.0 - - - +
713Q GLU* 1.3 63.4 + - - +
715Q LYS* 3.1 8.4 + - - +
716Q GLY* 3.0 18.9 + - - -
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Residues in contact with GLU 713 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673Q ILE* 6.0 6.1 - - + -
709Q SER 3.0 15.9 + - - +
710Q VAL* 3.7 6.1 - - - +
712Q GLN* 1.3 77.6 - - - +
714Q LEU* 1.3 62.7 + - - +
716Q GLY* 3.0 12.2 + - - -
717Q LEU* 3.2 12.0 + - - +
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Residues in contact with LEU 714 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710Q VAL 2.9 17.6 + - - +
711Q LEU* 4.0 4.5 - - - +
713Q GLU* 1.3 77.7 - - - +
715Q LYS* 1.3 52.1 + - - +
717Q LEU* 3.1 8.5 + - - +
718Q GLN* 2.7 35.9 + - - +
785Q VAL* 5.0 10.3 - - + +
788Q SER* 5.3 6.5 - - - -
789Q TYR* 4.9 17.9 - - - +
792Q LEU* 6.1 1.3 - - + -
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Residues in contact with LYS 715 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711Q LEU 2.9 15.6 + - - +
712Q GLN* 3.2 13.2 - - - +
713Q GLU 3.1 0.2 - - - -
714Q LEU* 1.3 78.3 - - - +
716Q GLY* 1.3 61.8 + - - +
718Q GLN* 3.1 7.6 + - - +
719Q GLU* 2.9 24.6 + - - +
789Q TYR* 5.6 4.2 - - - +
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Residues in contact with GLY 716 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556Q CYS* 5.5 7.0 - - - +
712Q GLN 3.0 9.0 + - - -
713Q GLU 3.0 8.5 + - - -
715Q LYS* 1.3 77.9 - - - +
717Q LEU* 1.3 60.9 + - - +
719Q GLU* 3.3 5.2 + - - +
720Q PHE* 3.0 22.7 + - - +
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Residues in contact with LEU 717 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556Q CYS* 5.8 4.0 - - - +
713Q GLU 3.2 9.7 + - - +
714Q LEU* 3.1 11.5 + - - +
716Q GLY* 1.3 72.0 - - - +
718Q GLN* 1.3 65.9 + - - +
720Q PHE* 3.0 8.2 + - - +
721Q LEU* 2.9 25.9 + - - +
785Q VAL* 5.4 9.6 - - + -
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Residues in contact with GLN 718 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714Q LEU 2.7 20.7 + - - +
715Q LYS* 3.1 9.2 + - - +
717Q LEU* 1.3 74.1 - - - +
719Q GLU* 1.3 56.7 + - - +
721Q LEU* 3.4 3.0 + - - +
722Q ASP* 2.9 30.9 + - - +
785Q VAL* 5.0 11.2 - - + +
786Q ARG* 5.2 11.2 - - + +
789Q TYR* 5.0 13.7 - - + -
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Residues in contact with GLU 719 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715Q LYS 2.9 16.1 + - - +
716Q GLY* 3.7 5.6 - - - +
718Q GLN* 1.3 76.2 - - - +
720Q PHE* 1.3 64.6 + - - +
722Q ASP* 3.6 6.4 - - - +
723Q ARG* 2.9 25.9 + - - +
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Residues in contact with PHE 720 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556Q CYS* 5.4 10.5 - - + -
716Q GLY 3.0 14.3 + - - +
717Q LEU* 3.0 12.3 + - - +
719Q GLU* 1.3 77.2 - - - +
721Q LEU* 1.3 62.6 + - - +
723Q ARG* 3.2 5.8 + - - +
724Q ASN* 3.0 23.6 + - - +
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Residues in contact with LEU 721 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717Q LEU 2.9 15.1 + - - +
718Q GLN* 4.0 4.0 - - - +
720Q PHE* 1.3 74.4 - - - +
722Q ASP* 1.3 66.4 + - - +
724Q ASN* 3.3 3.5 - - - +
725Q SER* 2.9 29.0 + - - -
782Q GLN* 4.7 22.2 - - + -
785Q VAL* 6.0 3.8 - - + -
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Residues in contact with ASP 722 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718Q GLN 2.9 18.7 + - - +
719Q GLU* 3.6 7.9 - - - +
721Q LEU* 1.3 79.2 - - - +
723Q ARG* 1.3 64.9 + - - +
725Q SER* 3.5 15.6 + - - -
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Residues in contact with ARG 723 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719Q GLU 2.9 16.5 + - - +
720Q PHE* 3.6 5.4 - - - +
722Q ASP* 1.3 80.2 - - - +
724Q ASN* 1.4 59.2 + - + +
725Q SER 3.3 2.6 + - - -
726Q GLN* 4.6 4.0 + - - +
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Residues in contact with ASN 724 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720Q PHE 3.0 14.2 + - - +
721Q LEU* 3.3 5.3 - - - -
723Q ARG* 1.4 75.7 - - + +
725Q SER* 1.3 61.4 + - - +
726Q GLN* 3.3 2.9 - - - +
727Q PHE* 3.7 17.3 + - + +
728Q ALA* 3.9 10.0 + - - +
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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