Contacts of the helix formed by residues 498 - 509 (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 PHE 498 (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* 4.3 5.8 - + - -
494S ASN* 3.0 39.6 + - + +
497S MET* 1.3 93.0 - - + +
499S ILE* 1.3 70.9 + - + +
500S LEU 3.7 0.2 - - - -
501S GLU* 3.8 1.5 + - - +
502S GLN* 3.0 31.5 + - - +
514S PHE* 6.0 0.7 - - + -
517S PHE* 3.4 41.1 - + + -
519S LEU* 3.4 39.5 - - + -
709S GLY 4.2 4.3 - - - -
712S GLU* 3.3 36.6 - - + -
713S GLY* 3.7 10.5 - - - -
716S ILE* 5.1 3.6 - - + -
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Residues in contact with ILE 499 (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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491S GLN* 4.4 11.9 - - - +
494S ASN 3.9 4.5 - - - +
495S HIS* 3.1 55.1 + - + +
498S PHE* 1.3 80.4 - - + +
500S LEU* 1.3 67.1 + - - +
502S GLN* 3.2 8.1 + - - +
503S GLU* 3.0 30.9 + - - +
514S PHE* 5.6 6.7 - - - -
519S LEU 5.4 4.7 - - - +
520S ASP* 4.9 8.1 - - - +
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Residues in contact with LEU 500 (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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495S HIS* 2.8 45.7 + - + +
496S THR* 3.4 37.7 - - + +
499S ILE* 1.3 73.8 - - - +
501S GLU* 1.3 66.2 + - - +
503S GLU* 2.9 33.8 + - + +
504S GLU* 3.4 6.8 + - - +
507S ARG* 5.1 7.3 + - - +
675S ARG* 6.3 3.1 - - + -
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Residues in contact with GLU 501 (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* 5.5 2.1 - - - +
496S THR 4.2 8.8 + - - +
497S MET* 3.8 26.2 - - - +
498S PHE 3.8 2.6 + - - +
499S ILE 3.3 0.8 - - - -
500S LEU* 1.3 78.6 - - - +
502S GLN* 1.3 62.0 + - + +
504S GLU* 3.6 6.9 + - - +
505S TYR* 2.8 57.0 + - + +
716S ILE* 4.2 18.9 - - + +
721S PHE 4.1 0.3 - - - +
722S PRO* 4.2 13.6 - - - +
724S ARG* 2.6 32.7 + - - +
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Residues in contact with GLN 502 (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* 3.0 24.0 + - - +
499S ILE 3.2 4.4 + - - +
500S LEU 3.2 0.8 - - - -
501S GLU* 1.3 77.1 - - - +
503S GLU* 1.3 65.7 + - - +
505S TYR* 3.2 12.2 + - + +
506S GLN* 3.2 26.0 + - - +
512S TRP* 3.0 43.3 - - + +
514S PHE* 3.3 22.0 - - + -
515S ILE* 2.6 48.6 + - - +
517S PHE* 3.8 13.4 - - - -
716S ILE* 5.2 3.8 - - + +
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Residues in contact with GLU 503 (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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495S HIS* 5.6 0.3 + - - -
499S ILE* 3.0 32.1 + - - +
500S LEU* 2.9 20.7 + - + +
502S GLN* 1.3 75.3 - - - +
504S GLU* 1.3 52.0 + - - +
506S GLN* 2.8 21.7 + - - +
507S ARG* 2.8 60.0 + - - +
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Residues in contact with GLU 504 (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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500S LEU 3.4 6.0 + - - +
501S GLU* 3.9 9.0 - - - +
502S GLN 3.3 0.4 - - - -
503S GLU* 1.3 76.1 - - - +
505S TYR* 1.3 65.8 + - - +
507S ARG* 3.7 25.6 - - - +
508S GLU* 3.0 49.9 + - - +
724S ARG* 4.1 15.6 + - - +
773S LYS* 3.4 30.2 + - - -
775S PHE* 3.3 20.8 - - + -
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Residues in contact with TYR 505 (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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501S GLU* 2.8 52.7 + - + +
502S GLN* 3.2 15.6 + - - +
503S GLU 3.2 0.4 - - - -
504S GLU* 1.3 77.4 - - - +
506S GLN* 1.3 63.4 + - - +
509S GLY 3.2 2.9 + - - -
510S ILE* 3.0 58.2 + - + +
512S TRP* 3.7 32.8 - + + -
716S ILE* 4.2 16.2 - - + +
720S GLY* 3.6 2.5 - - - -
721S PHE* 2.8 37.4 + + + -
722S PRO* 3.7 0.5 - - - +
775S PHE* 3.5 29.4 - + - -
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Residues in contact with GLN 506 (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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502S GLN* 3.2 15.6 + - - +
503S GLU* 2.8 22.3 + - - +
505S TYR* 1.3 77.9 - - - +
507S ARG* 1.3 54.7 + - + +
509S GLY* 2.5 29.8 + - - -
510S ILE 5.7 0.7 - - - -
512S TRP* 4.4 21.4 + - - +
514S PHE* 4.6 23.5 - - - +
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Residues in contact with ARG 507 (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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500S LEU* 5.1 7.3 + - - +
503S GLU* 2.8 46.0 + - - +
504S GLU* 3.7 27.9 + - - +
506S GLN* 1.3 73.0 - - + +
508S GLU* 1.3 64.6 + - + +
509S GLY* 2.9 2.4 + - - -
771S GLN* 5.2 3.8 - - - +
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Residues in contact with GLU 508 (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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504S GLU* 3.0 30.5 + - - +
505S TYR 4.4 2.0 - - - +
507S ARG* 1.3 78.9 - - - +
509S GLY* 1.3 63.1 + - - +
510S ILE* 4.4 1.1 - - + -
770S GLY* 3.8 4.6 - - - -
771S GLN* 2.9 47.8 + - - +
772S SER* 2.8 41.1 + - - -
773S LYS* 3.5 20.8 + - + -
775S PHE* 3.3 31.9 - - + -
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Residues in contact with GLY 509 (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 3.2 2.0 + - - -
506S GLN* 2.5 26.7 + - - -
507S ARG 2.9 1.7 - - - -
508S GLU* 1.3 75.9 - - - +
510S ILE* 1.3 64.1 + - - +
511S GLU 4.2 0.2 + - - -
769S ILE 5.1 1.6 - - - +
770S GLY* 5.3 0.9 - - - -
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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
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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