Contacts of the helix formed by residues 644 - 650 (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 HIS 644 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A TRP* 3.4 27.3 - + - -
651A THR* 3.9 18.2 - - + -
601B MET* 3.6 24.4 - - + -
605B GLN* 2.7 28.2 + - - +
630B ARG* 3.1 20.5 + - - -
642B ASP* 2.9 2.8 + - - -
643B GLY* 1.3 81.4 - - - +
645B SER* 1.3 67.3 + - - +
646B HIS 3.1 3.4 - - - -
647B ILE* 2.9 20.9 + - - +
648B GLN* 3.3 29.2 + - - +
803B TYR* 3.4 2.9 - - - -
804B MET* 3.3 24.0 - - + -
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Residues in contact with SER 645 (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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600B SER 4.2 9.9 - - - -
601B MET* 5.6 0.4 - - - -
604B PHE* 4.0 8.3 - - - -
605B GLN 6.1 0.2 - - - -
642B ASP* 2.7 35.5 + - - -
644B HIS* 1.3 73.1 - - - +
646B HIS* 1.3 58.6 + - - +
648B GLN* 3.3 18.3 + - - +
649B SER* 2.8 29.1 + - - -
688B TYR* 2.5 31.0 + - - -
690B THR* 3.9 5.2 - - - +
803B TYR* 4.0 2.7 - - - -
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Residues in contact with HIS 646 (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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644B HIS 3.1 1.2 - - - -
645B SER* 1.3 81.0 + - - +
647B ILE* 1.3 59.6 + - + +
649B SER* 3.2 5.9 + - - -
650B LEU* 3.1 32.5 + - - +
657B SER* 3.5 26.8 - - - -
658B TYR 3.2 24.8 + - - -
659B ASP* 3.6 11.9 + - + -
688B TYR* 4.0 6.2 - + - -
690B THR* 2.8 40.7 - - + +
762B THR* 4.3 2.2 + - - -
803B TYR* 3.7 25.4 - + + -
807B PHE* 3.5 37.0 - + + -
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Residues in contact with ILE 647 (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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647A ILE* 3.4 42.8 - - + +
650A LEU* 3.9 10.1 - - + -
651A THR* 3.7 11.2 - - + -
643B GLY 5.2 0.2 - - - +
644B HIS* 2.9 13.8 + - - +
646B HIS* 1.3 77.0 - - + +
648B GLN* 1.3 62.4 + - - +
650B LEU* 3.3 28.1 - - + +
651B THR* 3.5 1.6 - - - +
803B TYR* 5.8 0.2 - - + -
804B MET* 3.8 24.5 - - + -
806B LEU* 4.0 15.5 - - + -
807B PHE* 3.6 39.7 - - + +
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Residues in contact with GLN 648 (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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608A GLY* 6.0 1.2 - - - -
648A GLN* 4.3 25.4 + - + +
651A THR* 4.2 14.8 + - + -
604B PHE* 3.8 16.1 - - + +
605B GLN* 3.6 51.1 + - - +
644B HIS* 3.3 20.8 + - - +
645B SER* 3.3 25.6 - - - +
646B HIS 3.2 0.4 - - - -
647B ILE* 1.3 79.7 - - - +
649B SER* 1.3 59.9 + - - +
651B THR* 2.7 31.7 + - - -
652B ILE* 4.3 3.6 + - - +
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Residues in contact with SER 649 (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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604B PHE* 3.5 36.3 - - - -
645B SER 2.8 13.2 + - - -
646B HIS* 3.2 17.0 + - - -
647B ILE 3.4 0.2 - - - -
648B GLN* 1.3 73.1 - - - +
650B LEU* 1.3 61.1 + - - +
651B THR 3.1 7.1 + - - -
652B ILE* 3.3 20.9 + - - +
655B CYS* 4.1 7.3 - - - +
657B SER* 2.7 31.1 + - - -
688B TYR* 3.6 4.2 - - - -
766B ARG* 4.3 0.7 + - - -
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Residues in contact with LEU 650 (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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647A ILE* 4.0 6.3 - - + -
804A MET* 3.4 28.9 - - + +
806A LEU* 3.6 26.2 - - + -
646B HIS 3.1 18.4 + - - +
647B ILE* 3.3 33.9 - - + +
649B SER* 1.3 76.6 + - - +
651B THR* 1.3 61.1 + - - +
652B ILE 3.2 0.4 - - - -
657B SER* 5.0 0.7 - - - -
762B THR* 3.5 28.0 - - + +
766B ARG* 3.2 23.4 + - - +
807B PHE* 5.3 0.2 - - + -
810B GLN* 3.7 24.2 - - - +
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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