Contacts of the helix formed by residues 672 - 682 (chain N) in PDB entry 6LTJ
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 672 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358I PRO 4.1 7.2 - - - +
359I ARG* 4.7 6.7 - - - +
360I GLY 3.3 24.9 - - - +
361I LEU* 3.6 29.4 - - + -
671N ASN* 1.3 90.2 - - - +
673N VAL* 1.3 67.2 + - + +
675N SER* 3.0 5.7 + - - +
676N THR* 2.3 39.3 + - - -
676O THR* 4.0 11.0 - - + +
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Residues in contact with VAL 673 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671N ASN* 5.2 4.7 - - - +
672N PRO* 1.3 88.6 - - + +
674N MET* 1.3 87.4 + - + +
676N THR* 3.2 2.9 + - - -
677N VAL* 3.0 37.0 + - + +
858N LEU* 4.7 23.8 - - + +
676O THR* 4.3 9.2 - - + -
680O LEU* 3.6 28.4 - - + +
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Residues in contact with MET 674 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637N LEU* 3.5 23.4 - - + +
641N ARG* 3.3 35.9 - - - +
671N ASN* 4.6 12.4 + - - +
672N PRO 3.5 0.2 - - - -
673N VAL* 1.3 95.2 - - + +
675N SER* 1.3 67.3 + - - +
677N VAL* 3.1 20.8 - - - +
678N ALA* 2.9 25.5 + - - +
858N LEU* 4.0 31.6 - - + +
861N ALA* 4.0 10.5 - - + -
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Residues in contact with SER 675 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I ILE* 4.6 0.3 - - - +
356I GLN* 3.2 30.4 + - - +
358I PRO* 3.0 17.8 + - - +
633N ASP* 5.7 8.3 - - - -
637N LEU* 4.9 1.5 - - - +
671N ASN* 3.0 20.4 + - - +
672N PRO 3.0 12.5 + - - -
674N MET* 1.3 79.8 - - - +
676N THR* 1.3 58.6 + - - +
678N ALA* 3.7 5.3 - - - +
679N PHE* 2.9 30.0 + - - +
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Residues in contact with THR 676 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358I PRO* 3.0 31.4 - - + +
672N PRO 2.3 27.3 + - - -
673N VAL 3.5 3.6 - - - -
675N SER* 1.3 77.9 + - - +
677N VAL* 1.3 58.5 + - - +
679N PHE* 3.4 1.2 + - - +
680N LEU* 2.9 47.3 + - + +
673O VAL* 4.2 10.3 - - + +
676O THR* 3.1 28.7 - - + +
677O VAL 4.7 2.0 - - - +
680O LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 677 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637N LEU* 3.6 17.7 - - + -
673N VAL* 3.0 20.9 + - + +
674N MET* 3.1 26.2 - - - +
676N THR* 1.3 74.8 - - - +
678N ALA* 1.3 58.3 + - - +
680N LEU* 3.8 1.0 - - - +
681N ALA* 2.8 32.3 + - - +
861N ALA* 3.6 38.1 - - + +
862N ALA* 4.3 1.3 - - - +
865N ALA* 3.8 12.8 - - + +
680O LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 678 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355I ILE* 4.3 4.3 - - + -
633N ASP* 4.2 8.5 - - + +
636N ILE* 3.3 38.1 - - + +
637N LEU* 3.7 18.6 - - + -
674N MET 2.9 17.5 + - - +
675N SER* 3.7 5.6 - - - +
677N VAL* 1.3 75.5 - - - +
679N PHE* 1.3 66.6 + - - +
681N ALA* 3.1 2.7 + - - -
682N SER* 2.9 19.9 + - - -
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Residues in contact with PHE 679 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353I THR* 3.5 19.7 - - + -
355I ILE* 3.6 18.6 - - - +
356I GLN 3.3 23.3 - - - +
357I LYS* 3.9 29.6 - - + -
358I PRO* 3.9 13.9 - - + -
675N SER 2.9 18.7 + - - +
676N THR 3.6 3.6 - - - +
678N ALA* 1.3 73.5 - - - +
680N LEU* 1.3 80.1 + - + +
682N SER* 2.9 28.8 + - - -
683N VAL* 3.7 6.1 + - + +
673O VAL* 4.2 7.9 - - + -
207Q LEU 4.0 16.2 - - - -
208Q SER 4.1 6.5 - - - -
209Q GLU* 3.7 27.4 - - + -
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Residues in contact with LEU 680 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676N THR* 2.9 38.2 + - + +
679N PHE* 1.3 92.7 - - + +
681N ALA* 1.3 59.2 + - - +
683N VAL* 3.1 30.1 + - + +
865N ALA* 3.7 39.9 - - + +
868N ALA* 3.3 14.2 - - + +
869N ALA* 4.9 7.2 - - + +
673O VAL* 4.0 6.1 - - + -
677O VAL* 4.3 20.6 - - + -
680O LEU* 5.7 0.4 - - + -
206Q ILE 5.7 0.4 - - - +
207Q LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 681 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620N TRP* 4.1 3.8 - - - -
636N ILE* 3.7 12.3 - - + +
640N LEU* 3.5 31.6 - - + -
677N VAL 2.8 20.0 + - - +
678N ALA* 3.1 5.1 + - - +
680N LEU* 1.3 75.2 - - - +
682N SER* 1.3 56.2 + - - +
683N VAL 3.4 2.0 - - - -
684N VAL* 3.7 19.6 - - - +
689N ALA* 3.9 10.4 - - + +
864N ALA* 5.7 1.3 - - + +
865N ALA* 5.1 4.2 - - - +
868N ALA* 4.3 9.8 - - + +
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Residues in contact with SER 682 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I THR* 2.4 46.5 + - - -
354I PRO* 5.1 0.2 - - - -
355I ILE* 3.4 22.4 - - - +
620N TRP* 3.8 26.3 + - - +
636N ILE* 3.6 12.3 - - - -
678N ALA 2.9 9.6 + - - -
679N PHE 2.9 15.1 + - - -
681N ALA* 1.3 78.1 - - - +
683N VAL* 1.3 57.3 + - - +
684N VAL 3.5 2.5 - - - -
211Q VAL* 3.3 7.3 - - - +
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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