Contacts of the helix formed by residues 705 - 712 (chain B) in PDB entry 1L8A
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 ALA 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B MET* 4.1 5.8 - - + -
702B PRO* 3.1 38.6 + - + +
703B GLU 3.3 1.2 + - - +
704B GLY* 1.3 76.8 - - - +
706B GLU* 1.3 65.2 + - - +
707B GLU 3.4 0.7 - - - -
708B GLY* 3.1 6.0 + - - +
709B ILE* 3.0 26.7 + - + +
714B TYR* 4.1 25.2 - - + -
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Residues in contact with GLU 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LEU* 3.6 24.6 - - + +
668B VAL* 3.7 8.8 - - + +
701B MET* 3.4 30.4 - - + +
704B GLY* 3.0 27.2 + - - +
705B ALA* 1.3 70.4 - - - +
707B GLU* 1.3 64.6 + - - +
709B ILE* 3.1 17.1 + - - +
710B ARG* 3.1 38.8 + - - +
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Residues in contact with GLU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B GLY 4.5 4.5 + - - +
705B ALA 3.4 0.4 - - - -
706B GLU* 1.3 78.4 + - - +
708B GLY* 1.3 58.6 + - - +
710B ARG* 2.8 41.0 + - - +
711B LYS* 2.8 72.6 + - + +
787B TYR* 4.3 4.5 - - + +
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Residues in contact with GLY 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B GLY 5.1 0.8 + - - -
705B ALA* 3.1 8.8 + - - +
707B GLU* 1.3 78.6 - - - +
709B ILE* 1.3 57.2 + - - +
711B LYS 4.4 0.2 - - - -
712B GLY 2.9 24.3 + - - -
713B ILE 3.0 25.2 + - - -
714B TYR* 4.2 8.3 - - - -
787B TYR* 3.5 19.6 + - - -
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Residues in contact with ILE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B TYR* 3.5 7.1 - - - -
664B TYR* 3.7 31.6 - - + -
665B GLU* 3.9 11.7 - - + +
668B VAL* 3.8 37.5 - - + -
669B ILE* 3.9 17.0 - - + -
701B MET* 4.1 10.1 - - + -
705B ALA* 3.0 20.4 + - + +
706B GLU 3.1 6.5 + - - +
708B GLY* 1.3 74.8 - - - +
710B ARG* 1.3 63.8 + - - +
714B TYR* 3.7 22.2 - - + -
759B THR* 2.6 33.8 + - + -
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Residues in contact with ARG 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LEU* 3.8 18.6 - - - +
658B TYR* 2.5 30.1 + - - -
668B VAL* 4.0 16.2 + - + +
669B ILE* 5.5 2.0 - - - +
671B HIS* 4.7 12.3 + - - -
672B ASP* 3.5 43.2 + - + +
706B GLU* 3.1 27.7 + - - +
707B GLU* 2.8 53.1 + - - +
709B ILE* 1.3 78.2 - - - +
711B LYS* 1.3 64.7 + - - +
712B GLY 3.4 0.2 + - - -
763B GLU* 5.2 2.3 - - - +
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Residues in contact with LYS 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B GLU* 2.8 52.3 + - + +
708B GLY 4.0 0.7 - - - +
710B ARG* 1.3 75.7 - - - +
712B GLY* 1.3 58.5 + - - +
763B GLU* 4.1 14.0 - - - +
764B LEU* 3.5 16.5 + - - +
767B ASP* 5.9 2.3 - - - +
787B TYR* 3.5 49.0 - - + +
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Residues in contact with GLY 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B GLY 2.9 3.8 + - - -
709B ILE 3.5 0.8 + - - -
710B ARG 3.3 3.0 - - - -
711B LYS* 1.3 80.7 - - - +
713B ILE* 1.3 64.1 + - - +
758B VAL* 3.2 3.8 - - - -
759B THR* 2.9 35.4 + - - -
760B SER* 3.2 23.6 + - - -
764B LEU* 3.5 9.9 - - - +
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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