Contacts of the helix formed by residues 750 - 759 (chain C) in PDB entry 3K23
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 750 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564C ASN 4.1 26.5 - - - +
565C MET* 4.2 11.7 - - + +
568C GLY* 4.3 14.6 - - - -
748C GLU* 3.8 19.5 - - + +
749C PHE* 1.3 88.9 - - - +
751C GLU* 1.3 67.9 + - - +
752C MET* 3.0 5.5 + - + +
753C LEU* 3.1 9.2 + - + +
754C ALA* 3.0 17.5 + - - +
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Residues in contact with GLU 751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750C PRO* 1.3 72.5 - - - +
752C MET* 1.3 57.9 + - - +
754C ALA* 3.1 10.0 + - + +
755C GLU* 2.9 42.5 + - + +
743F ALA* 5.7 1.4 - - - +
744F LEU* 3.5 39.0 + - + +
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Residues in contact with MET 752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C GLY* 3.8 23.3 - - - +
571C VAL* 3.7 32.1 - - + -
572C ILE* 3.4 20.4 - - + -
575C VAL* 4.9 3.1 - - + -
750C PRO* 3.0 3.6 + - + +
751C GLU* 1.3 79.8 - - - +
753C LEU* 1.3 63.7 + - - +
755C GLU* 3.4 3.8 + - - +
756C ILE* 3.3 27.3 + - + +
744F LEU* 3.5 28.7 - - + +
745F LEU* 4.6 15.3 - - - +
748F LEU* 3.4 33.4 - - + -
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Residues in contact with LEU 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C JZN 3.6 26.5 - - - -
564C ASN* 3.2 30.1 - - + +
567C GLY 4.1 1.8 - - - +
568C GLY* 3.9 15.7 - - - +
571C VAL* 4.0 19.7 - - + -
600C TRP* 4.0 29.4 - - + -
749C PHE* 4.1 21.3 - - + -
750C PRO* 3.1 11.9 + - + +
752C MET* 1.3 79.7 - - - +
754C ALA* 1.3 55.9 + - - +
756C ILE* 4.1 5.5 - - + +
757C ILE* 3.0 38.6 + - + +
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Residues in contact with ALA 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740C PHE* 4.3 20.9 - - + -
749C PHE 4.3 7.4 + - - +
750C PRO 3.0 14.2 + - - +
751C GLU* 3.1 16.4 + - + +
753C LEU* 1.3 74.6 - - - +
755C GLU* 1.3 60.8 + - + +
757C ILE* 3.2 4.3 + - - +
758C THR* 2.7 32.6 + - - -
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Residues in contact with GLU 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C GLN* 6.3 0.2 - - - -
751C GLU* 2.9 31.1 + - + +
752C MET* 3.8 5.4 - - - +
754C ALA* 1.3 72.2 - - - +
756C ILE* 1.3 58.8 + - + +
758C THR* 2.7 36.7 + - - -
759C ASN* 3.4 9.8 + - - +
742F ASN* 3.2 24.8 + - + +
743F ALA* 3.0 10.4 + - - +
744F LEU* 2.9 32.6 + - + +
745F LEU* 3.0 32.8 + - + +
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Residues in contact with ILE 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C VAL* 3.5 35.7 - - + -
596C LEU* 4.9 4.9 - - + +
597C GLN* 4.0 30.7 - - + +
600C TRP* 3.0 58.6 - - + +
752C MET* 3.3 23.3 + - + +
753C LEU* 4.1 5.6 - - + +
755C GLU* 1.3 80.3 - - + +
757C ILE* 1.3 60.6 + - - +
759C ASN* 3.7 4.9 + - - +
760C GLN* 3.7 17.2 + - - +
745F LEU* 4.9 11.4 - - + -
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Residues in contact with ILE 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C TRP* 5.0 12.1 - - + -
736C CYS* 4.5 11.9 - - - -
737C PHE* 3.0 49.9 - - + -
740C PHE* 3.4 52.3 - - + -
749C PHE* 3.6 23.3 - - + -
753C LEU* 3.0 24.2 + - + +
754C ALA 3.7 2.2 - - - +
755C GLU 3.0 0.2 + - - -
756C ILE* 1.3 75.8 - - - +
758C THR* 1.3 65.0 + - - +
760C GLN* 3.1 12.6 + - - +
761C ILE* 3.9 0.5 + - - +
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Residues in contact with THR 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740C PHE* 5.4 5.0 - - - -
754C ALA 2.7 24.5 + - - -
755C GLU* 2.7 18.7 + - - -
757C ILE* 1.3 74.1 - - - +
759C ASN* 1.3 62.5 + - - +
761C ILE* 3.9 6.4 + - - +
762C PRO* 3.3 21.7 - - - +
742F ASN* 5.7 2.5 - - - +
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Residues in contact with ASN 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C GLN* 3.4 26.6 + - + +
755C GLU 3.4 8.3 + - - +
756C ILE 3.7 5.8 + - - +
757C ILE 3.3 0.6 - - - -
758C THR* 1.3 82.0 + - - +
760C GLN* 1.3 59.8 + - - +
761C ILE 3.6 0.4 - - - -
762C PRO* 3.9 11.9 - - - +
763C LYS* 3.2 35.8 - - + +
742F ASN* 2.6 39.8 + - - +
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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