Contacts of the helix formed by residues 709 - 720 (chain S) in PDB entry 1I84
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 GLY 709 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493S PHE* 4.0 7.9 - - - -
498S PHE* 4.2 0.5 - - - -
519S LEU* 4.0 16.3 - - - +
705S LEU 4.0 0.4 + - - -
706S ARG 3.4 11.4 + - - -
707S CYS 3.5 0.8 - - - -
708S ASN* 1.3 79.5 - - - +
710S VAL* 1.3 51.5 + - - +
712S GLU* 2.8 24.6 - - - +
713S GLY* 2.7 34.0 + - - -
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Residues in contact with VAL 710 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S MET* 5.9 0.7 - - + -
100S VAL* 4.6 7.0 - - + -
117S SER* 4.4 4.7 - - - -
120S PHE* 3.4 23.8 - - + -
122S VAL* 4.6 10.5 - - + -
683S ARG* 5.4 6.5 - - + -
685S ILE* 5.3 1.1 - - + -
705S LEU* 3.5 49.1 + - + +
708S ASN* 4.3 12.1 - - + +
709S GLY* 1.3 74.3 - - - +
711S LEU* 1.3 77.1 + - + +
713S GLY* 2.7 13.7 + - - -
714S ILE* 3.0 28.9 + - + +
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Residues in contact with LEU 711 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S LEU* 3.8 17.2 - - + +
96S ASN* 3.7 19.1 - - - +
97S GLU* 4.7 15.0 - - + +
100S VAL* 3.3 41.1 - - + -
705S LEU* 3.9 23.1 - - + +
706S ARG* 6.4 0.2 - - + -
710S VAL* 1.3 77.4 - - + +
712S GLU* 1.3 64.4 + - + +
714S ILE* 2.6 29.2 + - + +
715S ARG* 2.9 15.8 + - + +
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Residues in contact with GLU 712 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498S PHE* 3.3 28.9 - - + -
517S PHE* 3.6 28.4 - - + +
519S LEU* 4.0 14.9 - - + +
705S LEU 5.1 1.1 - - - +
706S ARG* 4.6 7.3 - - - +
709S GLY* 2.8 32.4 - - - +
710S VAL 3.5 0.2 + - - -
711S LEU* 1.3 73.2 + - + +
713S GLY* 1.3 52.9 + - - +
714S ILE 2.7 15.3 + - - -
715S ARG* 2.9 18.7 + - - +
716S ILE* 3.5 9.5 + - - +
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Residues in contact with GLY 713 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120S PHE* 3.0 29.0 - - - -
493S PHE* 4.4 0.9 - - - -
497S MET* 4.3 9.6 - - - +
498S PHE* 3.7 12.0 - - - -
709S GLY 2.7 17.8 + - - -
710S VAL 2.7 8.2 + - - -
712S GLU* 1.3 75.6 - - - +
714S ILE* 1.3 56.2 + - - +
716S ILE* 4.1 4.0 - - - +
717S CYS* 3.0 17.0 - - - -
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Residues in contact with ILE 714 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89S MET* 4.2 14.1 - - + -
90S ALA* 3.7 30.3 - - + -
95S LEU* 3.8 27.8 - - + -
100S VAL* 5.1 3.6 - - + -
117S SER* 3.4 44.0 - - - -
120S PHE* 4.0 0.2 - - + -
710S VAL* 3.0 27.7 + - + +
711S LEU* 2.6 20.0 + - - +
712S GLU 2.7 0.2 + - - -
713S GLY* 1.3 73.1 - - - +
715S ARG* 1.3 64.9 + - - +
716S ILE 3.3 2.2 - - - -
717S CYS* 3.0 16.4 + - - +
718S ARG* 3.1 10.7 + - + +
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Residues in contact with ARG 715 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S LEU* 5.1 7.6 - - + -
515S ILE* 4.6 23.5 - - - +
517S PHE* 3.8 18.5 - - + -
711S LEU* 2.9 12.8 + - + +
712S GLU* 2.9 11.6 + - - +
714S ILE* 1.3 76.4 - - - +
716S ILE* 1.3 50.6 + - - +
718S ARG* 2.9 27.3 + - - +
719S GLN* 2.3 83.2 + - + +
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Residues in contact with ILE 716 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119S LEU* 5.3 1.8 - - + -
497S MET* 4.1 25.1 - - + +
498S PHE* 5.1 2.2 - - + -
501S GLU* 4.2 21.5 - - + +
502S GLN* 5.2 3.4 - - - +
505S TYR* 4.2 9.9 - - + +
512S TRP* 3.7 26.7 - - + -
517S PHE* 4.2 22.5 - - + -
712S GLU 3.5 5.9 + - - +
713S GLY* 4.1 16.4 - - - +
715S ARG* 1.3 79.8 - - - +
717S CYS* 1.3 68.2 + - - +
719S GLN* 3.8 4.9 - - + -
720S GLY* 2.6 45.0 + - - +
722S PRO* 4.1 3.6 - - + +
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Residues in contact with CYS 717 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S ALA* 4.8 6.5 - - + -
118S GLY* 3.6 28.5 - - - -
119S LEU* 3.5 31.2 - - + -
713S GLY 3.0 28.5 - - - -
714S ILE* 3.0 8.0 + - - +
716S ILE* 1.3 83.9 - - - +
718S ARG* 1.3 60.1 + - - +
720S GLY 4.0 1.4 - - - +
722S PRO* 3.7 19.6 - - + +
777S ARG* 5.5 0.2 - - - +
778S THR* 3.0 30.0 + - + +
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Residues in contact with ARG 718 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S ALA* 5.1 12.1 - - + +
95S LEU* 3.6 33.3 - - + +
714S ILE* 3.1 8.4 + - + +
715S ARG* 2.9 31.8 + - - +
717S CYS* 1.3 78.5 - - - +
719S GLN* 1.3 92.2 + - + +
720S GLY 3.9 1.6 - - - +
777S ARG* 3.8 13.9 + - - +
778S THR* 5.0 1.1 - - - -
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Residues in contact with GLN 719 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512S TRP* 4.2 13.2 - - + -
515S ILE* 5.9 3.8 - - + -
517S PHE* 5.4 3.6 - - + -
715S ARG* 2.3 89.5 + - + +
716S ILE* 3.8 7.4 - - + -
718S ARG* 1.3 92.7 + - + +
720S GLY* 1.3 55.3 + - - +
721S PHE* 4.2 2.9 - - - -
777S ARG* 2.8 26.2 + - - -
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Residues in contact with GLY 720 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505S TYR* 3.8 1.3 - - - -
512S TRP* 3.7 14.6 - - - -
716S ILE* 2.6 28.1 + - - +
717S CYS 4.0 1.4 - - - +
718S ARG 3.9 2.9 - - - +
719S GLN* 1.3 79.4 - - - +
721S PHE* 1.3 71.2 + - - -
722S PRO* 3.3 12.6 - - - +
777S ARG* 3.4 13.5 - - - -
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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