Contacts of the helix formed by residues 687 - 695 (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 LEU 687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A HIS* 3.1 31.9 - - + +
662A LEU* 3.8 21.3 - - + -
683A VAL* 3.0 36.4 + - + +
686A LEU* 1.3 79.3 - - - +
688A PRO* 1.4 70.6 - - + +
690A LEU* 3.3 11.3 - - - +
691A CYS* 3.2 31.6 - - - -
698A GLN* 4.1 30.1 - - + +
701A VAL* 4.3 24.9 - - + -
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Residues in contact with PRO 688 (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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660A HIS* 3.6 19.7 - - + -
684A GLN 4.2 2.9 - - - +
685A ARG 3.9 10.1 - - - +
686A LEU 3.7 2.0 - - - -
687A LEU* 1.4 91.2 - - + +
689A VAL* 1.3 54.8 + - + +
690A LEU 2.6 10.5 + - - -
691A CYS* 4.4 3.6 - - + +
692A GLN* 2.5 56.3 + - + +
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A ARG 4.3 9.4 - - - +
686A LEU* 3.5 29.2 + - + -
688A PRO* 1.3 75.8 - - + +
690A LEU* 1.3 57.3 + - - +
692A GLN* 4.7 4.7 - - - -
693A ALA* 3.1 24.9 - - + +
694A HIS* 4.1 1.4 + - - -
718A GLN* 4.1 23.2 + - + -
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Residues in contact with LEU 690 (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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686A LEU* 2.9 25.8 - - + +
687A LEU* 3.3 11.2 - - - +
688A PRO 2.6 5.9 + - - -
689A VAL* 1.3 76.3 - - - +
691A CYS* 1.3 59.0 + - - +
694A HIS* 2.7 44.1 + - + +
695A GLY 2.9 6.4 + - - -
696A LEU* 3.3 28.0 - - + +
701A VAL* 3.4 28.3 - - + -
704A ILE* 6.4 0.7 - - + -
714A LEU* 4.8 10.3 - - + -
717A VAL* 4.3 9.9 - - + -
718A GLN* 3.1 38.4 - - - +
721A LEU* 5.4 0.7 - - + -
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Residues in contact with CYS 691 (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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687A LEU* 3.2 30.7 - - - +
688A PRO* 3.0 3.7 + - + +
690A LEU* 1.3 75.6 - - - +
692A GLN* 1.3 60.9 + - - +
693A ALA 3.0 9.3 + - - -
695A GLY* 3.4 22.4 + - - +
696A LEU 3.1 22.9 - - - +
697A THR 4.7 2.5 - - - -
698A GLN* 4.8 9.4 - - - -
701A VAL* 6.2 0.2 - - - -
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Residues in contact with GLN 692 (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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688A PRO* 2.5 37.6 + - - +
689A VAL* 4.6 2.2 - - - +
691A CYS* 1.3 72.5 - - - +
693A ALA* 1.3 58.4 + - - +
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Residues in contact with ALA 693 (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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688A PRO 4.0 0.2 + - - -
689A VAL* 3.1 29.2 - - + +
690A LEU 3.9 1.2 - - - -
691A CYS 3.0 1.0 - - - -
692A GLN* 1.3 81.7 - - - +
694A HIS* 1.3 75.4 + - + +
695A GLY 3.6 1.6 - - - -
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Residues in contact with HIS 694 (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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689A VAL 4.1 2.8 + - - -
690A LEU* 2.7 31.5 + - + +
693A ALA* 1.3 89.0 + - + +
695A GLY* 1.3 66.2 + - - +
696A LEU* 2.7 18.4 + - + +
718A GLN* 3.1 36.8 + - - +
721A LEU* 3.3 42.3 - - + +
722A PRO* 3.7 20.0 - - + -
732A PRO* 4.2 14.8 - - + +
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Residues in contact with GLY 695 (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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690A LEU 2.9 3.6 + - - -
691A CYS* 3.4 21.6 + - - -
693A ALA 3.6 1.4 - - - -
694A HIS* 1.3 79.2 - - - +
696A LEU* 1.3 58.2 + - - +
697A THR* 3.9 2.8 + - - +
700A GLN* 4.7 1.4 - - - +
732A PRO* 5.3 3.1 - - - +
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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