Contacts of the helix formed by residues 671 - 681 (chain A) in PDB entry 4OLM
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 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A ILE* 1.3 69.1 + - + +
673A PHE* 3.2 3.1 - - - -
674A LEU* 2.7 37.7 + - + +
675A ASN* 2.8 28.0 + - - +
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Residues in contact with ILE 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A PRO* 1.3 84.7 - - + +
673A PHE* 1.3 69.1 + - + +
675A ASN* 3.0 20.3 + - + +
676A VAL* 2.9 34.4 + - + +
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Residues in contact with PHE 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A PRO 3.0 2.1 + - - -
672A ILE* 1.3 83.3 - - + +
674A LEU* 1.3 59.0 + - + +
676A VAL* 3.2 22.1 - - - +
677A LEU* 3.2 31.1 + - + +
723A PRO* 3.3 26.7 - - + -
806A CYS* 5.0 1.1 - - - -
833A ASN* 5.6 4.9 - - + -
834A TYR* 3.4 55.2 - + - -
837A GLU* 3.6 52.3 - - + +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A PRO* 2.7 20.6 + - + +
673A PHE* 1.3 72.1 - - + +
675A ASN* 1.3 66.5 + - - +
676A VAL 3.0 1.8 - - - -
677A LEU* 3.0 11.8 + - + +
678A GLU* 2.8 49.9 + - - +
802A GLN* 3.6 43.1 - - + +
805A LEU* 3.8 16.2 - - + -
841A ILE* 4.2 22.0 - - + -
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Residues in contact with ASN 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A PRO* 2.8 33.8 - - - +
672A ILE* 3.0 23.3 - - - +
674A LEU* 1.3 73.6 - - - +
676A VAL* 1.3 64.0 + - + +
678A GLU* 3.8 11.5 + - - +
679A ALA* 3.0 24.8 + - - +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A ILE* 2.9 27.7 + - + +
673A PHE* 3.2 12.6 - - - +
674A LEU 3.0 0.2 - - - -
675A ASN* 1.3 74.5 - - + +
677A LEU* 1.3 66.2 + - + +
679A ALA* 2.7 23.6 + - - +
680A ILE* 2.8 25.7 + - + +
721A ALA 4.2 11.9 - - - +
723A PRO* 3.7 34.5 - - + -
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Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A PHE* 3.2 33.1 + - + +
674A LEU* 3.0 11.9 + - + +
676A VAL* 1.3 79.2 - - - +
678A GLU* 1.3 64.0 + - - +
680A ILE* 3.4 8.3 + - + +
681A GLU* 3.0 29.3 + - - +
718A TRP* 4.9 4.0 - - - +
722A LEU* 3.9 27.8 - - + -
723A PRO* 4.5 10.5 - - + -
805A LEU* 4.0 20.4 - - + +
806A CYS* 4.1 33.0 - - + +
809A ALA* 4.1 15.7 - - + -
834A TYR* 4.8 2.2 - - + -
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Residues in contact with GLU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A LEU* 2.8 55.2 + - - +
675A ASN* 3.9 8.6 + - - +
677A LEU* 1.3 74.5 - - - +
679A ALA* 1.3 62.4 + - - +
681A GLU* 3.3 15.9 + - - +
802A GLN* 3.9 18.6 + - - +
805A LEU* 3.8 15.9 - - + +
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Residues in contact with ALA 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A ASN 3.0 20.2 + - - +
676A VAL* 2.7 12.2 + - - +
678A GLU* 1.3 74.1 - - - +
680A ILE* 1.3 64.3 + - + +
681A GLU 3.4 3.3 + - - +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A VAL* 2.8 34.1 + - + +
677A LEU* 3.4 17.0 - - + +
679A ALA* 1.3 76.2 - - + +
681A GLU* 1.3 64.2 + - - +
682A PRO* 3.2 5.2 - - - +
718A TRP* 3.5 36.0 - - + +
721A ALA* 3.8 28.9 - - + +
722A LEU* 3.0 37.5 - - + -
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A LEU* 3.0 16.6 + - - +
678A GLU* 3.4 13.1 - - - +
679A ALA 3.2 6.2 - - - +
680A ILE* 1.3 75.4 - - - +
682A PRO* 1.3 85.3 - - + +
683A GLY* 3.5 2.1 + - - -
718A TRP* 4.0 4.7 + - - -
748A ALA* 5.7 0.9 - - - +
804A PHE* 3.7 10.6 - - + -
805A LEU* 3.6 24.4 - - + +
808A LYS* 3.2 35.6 + - - -
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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