Contacts of the helix formed by residues 799 - 808 (chain A) in PDB entry 3UGM
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 THR 799 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A LEU* 5.3 3.4 - - - +
798A LEU* 1.3 83.8 - - - +
800A GLN* 1.3 71.6 + - - +
801A GLU* 3.2 7.8 + - - +
802A GLN* 2.7 47.5 + - + +
803A VAL* 3.0 29.7 + - - +
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Residues in contact with GLN 800 (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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762A HIS* 2.7 31.9 + - - +
763A GLY* 3.1 16.3 + - - +
764A LEU* 3.1 25.8 - - + +
768A GLN* 4.7 6.1 - - - +
789A LEU* 4.7 21.3 - - + +
799A THR* 1.3 79.5 + - - +
801A GLU* 1.3 68.2 + - - +
802A GLN 3.1 1.1 - - - -
803A VAL* 4.0 3.4 - - - +
804A VAL* 2.8 31.1 + - - +
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Residues in contact with GLU 801 (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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768A GLN* 3.7 25.0 + - - +
799A THR* 3.2 6.0 + - - +
800A GLN* 1.3 82.1 - - - +
802A GLN* 1.3 59.0 + - + +
804A VAL* 4.0 3.1 - - - +
805A ALA* 3.2 24.9 + - - +
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Residues in contact with GLN 802 (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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798A LEU* 3.2 32.8 - - + +
799A THR* 2.7 41.9 + - + +
801A GLU* 1.3 79.4 - - + +
803A VAL* 1.3 59.5 + - - +
805A ALA* 3.5 6.4 - - - +
806A ILE* 3.4 27.9 + - - +
834A PRO* 4.9 2.4 + - - +
835A ASP* 4.8 12.5 + - - +
838A VAL* 3.7 26.9 - - + +
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Residues in contact with VAL 803 (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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764A LEU* 5.8 1.6 - - + -
785A VAL* 4.2 22.0 - - + -
789A LEU* 4.3 32.5 - - + +
798A LEU* 3.5 32.1 - - + -
799A THR 3.0 24.3 + - - +
800A GLN* 3.2 3.3 + - - +
802A GLN* 1.3 74.4 - - - +
804A VAL* 1.3 71.4 + - - +
805A ALA 2.9 2.0 + - - -
806A ILE* 3.1 13.8 + - + +
807A ALA* 3.2 10.9 + - - +
816A LEU* 4.4 18.4 - - + -
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Residues in contact with VAL 804 (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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764A LEU* 3.6 25.6 - - + -
768A GLN* 3.7 50.0 - - + +
771A ALA* 4.9 5.2 - - + -
772A ILE* 4.0 16.0 - - + +
785A VAL* 5.7 1.1 - - - -
800A GLN* 2.8 22.4 + - - +
801A GLU* 4.0 3.8 - - - +
803A VAL* 1.3 73.7 - - - +
805A ALA* 1.3 59.4 + - - +
807A ALA* 3.3 1.7 + - - +
808A SER* 2.4 39.0 + - - +
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Residues in contact with ALA 805 (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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801A GLU 3.2 18.4 + - - +
802A GLN* 3.5 10.1 - - - +
803A VAL 2.9 1.6 + - - -
804A VAL* 1.3 79.9 - - - +
806A ILE* 1.3 64.6 + - - +
808A SER* 2.9 23.4 + - - -
809A ASN* 4.1 8.0 + - - -
838A VAL* 5.9 0.7 - - + -
842A SER* 4.1 18.0 - - - +
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Residues in contact with ILE 806 (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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798A LEU* 4.6 13.5 - - + -
802A GLN 3.4 9.5 + - - +
803A VAL* 3.1 8.4 + - + +
805A ALA* 1.3 76.4 - - - +
807A ALA* 1.3 59.5 + - - +
808A SER 3.4 0.6 + - - -
809A ASN* 4.2 6.5 + - - -
812A GLY 4.5 1.6 + - - -
815A ALA* 3.7 31.9 - - + +
816A LEU* 4.1 22.7 - - + +
819A VAL* 4.0 22.0 - - + -
838A VAL* 3.8 46.2 - - + +
841A ALA* 3.9 15.5 - - + +
842A SER* 3.9 11.4 + - - +
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Residues in contact with ALA 807 (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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772A ILE* 3.2 28.7 - - + +
775A ASN* 4.2 1.7 + - - -
781A ALA* 3.7 8.5 - - + +
785A VAL* 4.1 7.6 - - + -
803A VAL 3.2 12.1 + - - +
805A ALA 2.9 1.2 + - - -
806A ILE* 1.3 75.8 - - - +
808A SER* 1.3 63.9 + - - +
809A ASN 3.2 6.3 + - - +
812A GLY* 3.4 23.8 - - - +
816A LEU* 3.8 25.6 - - + -
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Residues in contact with SER 808 (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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771A ALA* 4.1 16.0 + - - +
772A ILE* 4.4 2.5 - - - +
775A ASN* 2.4 39.2 + - - +
804A VAL* 2.4 34.0 + - - +
805A ALA* 2.9 13.3 + - - -
807A ALA* 1.3 75.0 - - - +
809A ASN* 1.3 58.1 + - - +
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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