Contacts of the helix formed by residues 661 - 675 (chain D) in PDB entry 1SO2
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 661 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659D LEU* 3.1 12.5 - - + -
660D ASP* 1.3 78.2 - - - +
662D ILE* 1.3 60.1 + - - +
664D VAL* 3.1 27.3 - - + +
665D GLU* 3.8 10.2 + - - +
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Residues in contact with ILE 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D LEU* 3.8 13.1 + - + +
661D LEU* 1.3 77.5 - - - +
663D LEU* 1.3 65.9 + - - +
664D VAL 3.0 1.8 - - - -
665D GLU* 3.0 28.7 + - - +
666D GLU* 3.1 15.6 + - - +
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Residues in contact with LEU 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D LEU 4.7 1.2 + - - -
660D ASP* 3.9 19.1 + - + +
661D LEU 3.5 0.4 - - - -
662D ILE* 1.3 77.4 - - - +
664D VAL* 1.3 66.9 + - + +
666D GLU* 3.0 27.7 + - + +
667D TYR* 3.0 28.9 + - + +
701D TYR* 6.1 5.2 - - + -
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Residues in contact with VAL 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660D ASP 3.3 17.0 - - - +
661D LEU* 3.1 23.3 - - + +
663D LEU* 1.3 82.4 - - + +
665D GLU* 1.3 62.3 + - + +
667D TYR* 3.0 8.9 + - + +
668D ASP* 2.7 43.2 + - - +
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Residues in contact with GLU 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661D LEU 4.0 13.0 - - - +
662D ILE* 3.0 16.9 + - - +
664D VAL* 1.3 81.2 - - + +
666D GLU* 1.3 63.7 + - + +
668D ASP* 3.4 7.4 + - - +
669D SER* 2.9 28.1 + - - -
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Residues in contact with GLU 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D ILE* 3.1 10.6 + - - +
663D LEU* 3.0 38.8 + - + +
665D GLU* 1.3 77.0 - - - +
667D TYR* 1.3 63.8 + - - +
669D SER* 3.2 3.6 + - - -
670D LEU* 3.0 27.6 + - - +
698D GLN* 6.0 0.2 + - - -
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Residues in contact with TYR 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D LEU* 3.0 16.4 + - + +
664D VAL* 3.5 9.2 - - + +
666D GLU* 1.3 78.3 - - - +
668D ASP* 1.3 72.8 + - - +
670D LEU* 3.8 5.5 - - - +
671D ILE* 2.9 53.8 + - + +
701D TYR* 4.7 11.0 - + - -
702D THR* 3.7 37.7 - - + -
705D GLN* 3.7 27.8 + - + -
706D ASP* 3.3 32.9 + - - +
790D LYS* 4.9 5.7 - - - +
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Residues in contact with ASP 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664D VAL* 2.7 39.2 + - - +
665D GLU* 3.9 6.6 + - - +
667D TYR* 1.3 88.1 - - - +
669D SER* 1.3 61.4 + - - +
671D ILE* 3.7 6.4 - - - +
672D GLU* 2.8 29.1 + - - +
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Residues in contact with SER 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665D GLU 2.9 18.8 + - - -
666D GLU* 3.6 4.5 - - - -
668D ASP* 1.3 71.8 - - - +
670D LEU* 1.3 55.3 + - - +
672D GLU* 2.8 16.0 + - - +
673D LYS* 2.7 58.1 + - - +
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Residues in contact with LEU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D GLU 3.0 14.1 + - - +
667D TYR* 3.8 5.8 - - - +
669D SER* 1.3 80.0 + - - +
671D ILE* 1.3 56.9 + - - +
673D LYS* 3.1 10.1 + - - +
674D MET* 2.8 59.3 + - + +
679D PHE* 4.5 10.3 - - + -
684D LEU* 4.4 21.8 - - + -
698D GLN* 5.0 8.7 - - + +
699D VAL* 4.9 9.4 - - + -
702D THR* 3.6 26.9 - - + +
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Residues in contact with ILE 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D TYR* 2.9 48.4 + - + +
668D ASP* 3.7 7.6 - - - +
670D LEU* 1.3 76.7 - - - +
672D GLU* 1.3 58.1 + - - +
674D MET* 3.5 4.8 + - + +
675D SER* 2.4 35.9 + - - +
702D THR* 3.5 24.0 - - + -
703D LEU* 5.0 7.2 - - + -
706D ASP* 3.6 31.0 - - + +
750D TRP* 5.3 4.1 - - + -
791D SER* 3.9 21.5 - - - -
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Residues in contact with GLU 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D ASP 2.8 16.0 + - - +
669D SER* 2.8 19.5 + - - +
671D ILE* 1.3 78.1 - - - +
673D LYS* 1.3 73.2 + - - +
675D SER* 3.4 16.9 + - - -
676D ASN* 4.3 2.4 + - - +
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Residues in contact with LYS 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D SER* 2.7 34.8 + - - +
670D LEU* 3.3 14.1 - - - +
672D GLU* 1.3 82.9 - - - +
674D MET* 1.3 59.2 + - - +
675D SER 3.1 4.9 + - - -
676D ASN* 3.3 18.2 + - - +
679D PHE* 3.7 30.7 - - + -
680D PRO* 4.2 17.0 - - + +
683D GLU* 5.5 7.8 + - - +
684D LEU* 5.0 18.8 - - + +
687D LYS* 4.8 15.8 - - - +
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Residues in contact with MET 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670D LEU* 2.8 44.9 + - + +
671D ILE* 3.8 5.4 - - + +
673D LYS* 1.3 68.9 - - - +
675D SER* 1.3 56.1 + - - +
676D ASN 3.0 9.5 + - - +
679D PHE* 3.6 30.1 - - + -
699D VAL* 3.6 26.7 - - + -
702D THR* 4.7 7.2 - - - -
703D LEU* 3.3 35.9 - - + -
747D HIS* 3.0 42.1 + - + -
750D TRP* 3.5 16.0 - - + -
751D TYR* 4.1 0.7 - - - -
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Residues in contact with SER 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671D ILE* 2.4 26.8 + - - +
672D GLU* 3.6 12.3 - - - -
673D LYS 3.0 1.4 - - - -
674D MET* 1.3 77.4 - - - +
676D ASN* 1.3 57.7 + - - +
750D TRP* 4.5 1.4 - - - -
751D TYR* 3.4 17.4 + - - -
755D ARG* 3.9 16.5 + - - +
791D SER* 3.7 26.1 + - - -
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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