Contacts of the helix formed by residues 732 - 740 (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 PRO 732 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A HIS* 4.2 19.3 - - + +
695A GLY 5.3 2.5 - - - +
696A LEU* 4.2 12.6 - - + -
700A GLN* 3.8 18.2 - - - +
721A LEU* 4.8 11.0 - - + -
725A CYS* 4.9 7.6 - - + -
731A THR* 1.4 90.0 - - - +
733A ALA* 1.3 54.8 + - - +
735A VAL* 2.6 33.7 + - + +
736A VAL* 3.0 10.1 + - - +
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Residues in contact with ALA 733 (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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700A GLN* 4.0 12.3 - - - +
731A THR* 2.9 14.4 + - - +
732A PRO* 1.3 73.9 - - - +
734A GLN* 1.3 55.0 + - + +
736A VAL* 3.2 3.6 + - - +
737A ALA* 2.6 40.5 + - + +
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Residues in contact with GLN 734 (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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729A GLY 4.0 1.0 - - - +
730A LEU* 3.1 41.5 - - + +
731A THR* 3.4 13.9 + - - +
732A PRO 3.0 0.8 + - - -
733A ALA* 1.3 78.6 - - + +
735A VAL* 1.3 61.5 + - - +
737A ALA* 4.1 7.0 - - - -
738A ILE* 3.4 11.6 + - - +
767A ASP* 2.5 34.8 + - - +
770A VAL* 3.2 44.4 - - + +
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Residues in contact with VAL 735 (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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717A VAL* 3.8 17.0 - - + -
720A LEU 4.9 1.1 - - - +
721A LEU* 4.3 38.4 - - + -
724A LEU* 4.7 7.4 - - + -
725A CYS* 4.9 0.9 - - - -
730A LEU* 4.4 17.7 - - + -
731A THR 3.6 16.6 - - - +
732A PRO 2.6 14.9 + - - +
734A GLN* 1.3 72.7 - - - +
736A VAL* 1.3 55.8 + - + +
738A ILE* 3.1 7.0 + - - +
739A ALA* 2.7 36.6 + - - +
748A LEU* 3.6 22.7 - - + -
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Residues in contact with VAL 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LEU* 4.1 24.5 - - + -
700A GLN* 3.3 53.6 - - + +
703A ALA* 5.3 2.5 - - + -
704A ILE* 4.1 12.3 - - + -
717A VAL* 6.2 0.2 - - + -
732A PRO 3.0 6.8 + - - +
733A ALA* 3.8 4.5 - - - +
735A VAL* 1.3 80.5 - - + +
737A ALA* 1.3 62.4 + - - +
739A ALA* 4.1 6.3 - - - -
740A SER* 2.9 35.8 + - - +
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Residues in contact with ALA 737 (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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733A ALA 2.6 24.8 + - - +
734A GLN* 4.2 6.3 - - + -
736A VAL* 1.3 74.2 - - - +
738A ILE* 1.3 63.0 + - - +
739A ALA 3.2 0.7 + - - -
740A SER* 3.6 4.1 + - - -
741A HIS* 3.5 19.4 + - - -
770A VAL* 5.8 1.3 - - + +
774A SER* 2.9 14.7 + - - +
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Residues in contact with ILE 738 (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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730A LEU* 5.8 1.1 - - + -
734A GLN 3.4 11.0 + - - +
735A VAL* 3.1 1.9 + - - +
737A ALA* 1.3 80.2 - - - +
739A ALA* 1.3 61.1 + - - +
740A SER 3.7 0.5 + - - -
741A HIS* 4.7 4.3 + - - +
744A GLY* 4.7 1.2 - - - +
747A ALA* 3.8 17.5 - - + +
748A LEU* 3.5 34.8 - - + +
751A VAL* 4.1 19.5 - - + -
770A VAL* 3.5 29.6 - - + +
773A ALA* 3.0 48.7 - - + +
774A SER* 2.9 16.6 + - - +
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Residues in contact with ALA 739 (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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704A ILE* 4.1 11.9 - - + +
707A ASN* 5.8 0.3 - - - +
713A ALA* 4.1 9.4 - - + +
717A VAL* 3.7 27.8 - - + -
735A VAL 2.7 19.9 + - - +
736A VAL* 3.0 8.0 + - - +
738A ILE* 1.3 77.3 - - - +
740A SER* 1.3 59.0 + - - +
741A HIS 3.5 3.0 + - - +
744A GLY* 3.3 20.6 + - - -
748A LEU* 3.8 13.7 - - + -
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Residues in contact with SER 740 (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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703A ALA* 2.4 32.9 + - - +
704A ILE* 3.2 12.9 - - - +
707A ASN* 2.7 22.3 + - - +
736A VAL* 2.9 21.3 + - - +
737A ALA* 3.6 2.3 + - - -
738A ILE 3.6 2.4 - - - -
739A ALA* 1.3 73.5 - - - +
741A HIS* 1.3 75.9 + - - +
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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