Contacts of the helix formed by residues 679 - 687 (chain A) in PDB entry 2LNX
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 GLU 679 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A ASN 5.3 2.2 - - - +
678A MET* 1.3 73.1 - - - +
680A ARG* 1.3 59.3 - - - +
681A GLN* 3.3 5.5 - - + +
682A GLN* 3.3 34.2 + - + +
683A THR* 2.7 32.9 + - - -
698A ARG* 3.2 5.2 - - - -
700A ARG* 6.0 0.7 - - - +
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Residues in contact with ARG 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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679A GLU* 1.3 72.8 - - - +
681A GLN* 1.3 64.7 + - - +
683A THR* 3.3 12.9 + - - -
684A ASP* 3.5 13.8 + - - +
698A ARG* 3.1 23.3 - - - +
700A ARG* 6.0 0.6 - - - +
719A HIS* 4.8 14.2 - - + +
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Residues in contact with GLN 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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679A GLU* 3.3 5.5 - - + +
680A ARG* 1.3 79.7 - - - +
682A GLN* 1.3 63.2 + - - +
684A ASP* 3.4 15.0 + - - +
685A ASN* 3.1 45.4 + - - +
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Residues in contact with GLN 682 (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 ASN 5.4 2.9 - - - +
678A MET* 3.7 24.8 - - - +
679A GLU* 3.3 36.3 + - + +
681A GLN* 1.3 77.5 - - - +
683A THR* 1.3 58.8 + - - +
685A ASN* 3.4 7.5 + - - +
686A LEU* 2.9 47.6 + - - +
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Residues in contact with THR 683 (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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678A MET* 4.7 5.2 - - - -
679A GLU 2.7 16.9 + - - -
680A ARG 3.5 6.7 + - - -
681A GLN 3.3 0.2 - - - -
682A GLN* 1.3 76.7 - - - +
684A ASP* 1.3 63.1 + - - +
686A LEU* 3.2 20.1 + - - +
687A LEU* 3.3 12.2 + - + +
696A LEU* 4.4 7.4 - - + -
698A ARG* 2.9 30.3 + - - +
710A SER* 3.1 39.5 - - - +
717A VAL* 4.3 4.6 - - + +
719A HIS* 3.9 10.1 - - + -
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Residues in contact with ASP 684 (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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680A ARG* 3.5 9.6 + - - +
681A GLN* 3.4 20.2 + - - +
682A GLN 3.3 0.4 - - - -
683A THR* 1.3 79.7 - - - +
685A ASN* 1.3 61.4 + - - +
686A LEU 3.1 0.3 + - - -
687A LEU 3.3 1.9 + - - -
688A LYS* 2.9 36.2 + - - +
717A VAL* 4.3 21.6 - - - +
719A HIS* 5.5 4.1 + - + +
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Residues in contact with ASN 685 (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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681A GLN* 3.1 43.4 + - - +
682A GLN* 3.9 6.3 - - + +
684A ASP* 1.3 81.4 - - - +
686A LEU* 1.3 61.0 + - - +
688A LYS* 3.0 33.6 + - + +
689A SER* 5.8 0.2 - - - -
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Residues in contact with LEU 686 (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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678A MET* 4.0 25.8 - - + -
682A GLN* 2.9 26.9 + - - +
683A THR* 3.2 14.6 - - - +
685A ASN* 1.3 80.0 - - + +
687A LEU* 1.3 62.0 + - + +
688A LYS 3.3 1.4 + - - -
689A SER* 4.5 1.6 + - - -
690A HIS* 3.5 19.7 + - + +
696A LEU* 4.4 5.2 - - + -
767A TYR* 3.6 44.2 - - + +
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Residues in contact with LEU 687 (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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683A THR 3.3 6.8 + - - +
684A ASP 3.5 2.5 - - - -
686A LEU* 1.3 74.0 - - - +
688A LYS* 1.3 62.9 + - - +
689A SER 3.3 2.6 + - - -
690A HIS* 3.9 10.4 + - + -
694A THR* 3.2 45.1 - - + +
696A LEU* 3.5 26.7 - - + -
710A SER* 3.6 23.8 - - - +
711A ILE 4.0 9.4 - - - -
712A LYS* 3.4 34.7 - - + +
717A VAL* 3.3 37.6 - - + +
767A TYR* 4.8 0.7 - - + -
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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