Contacts of the helix formed by residues 672 - 683 (chain A) in PDB entry 4IQJ
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 SER 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A GLN 5.4 2.4 + - - -
670A LEU 3.5 1.6 - - - -
671A GLU* 1.3 79.3 + - - +
673A GLY* 1.3 57.3 + - - +
674A GLY 3.3 1.8 - - - -
675A MET* 3.0 18.7 + - - +
676A THR* 2.7 35.9 + - - -
697A TYR* 5.3 6.0 - - - -
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Residues in contact with GLY 673 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671A GLU 3.7 2.3 + - - -
672A SER* 1.3 74.3 - - - +
674A GLY* 1.3 61.6 + - - +
676A THR* 4.0 5.8 - - - -
677A ALA* 3.4 19.2 + - - +
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Residues in contact with GLY 674 (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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672A SER* 3.3 1.8 - - - -
673A GLY* 1.3 75.3 - - - +
675A MET* 1.3 61.8 + - - +
677A ALA* 3.4 7.5 + - - +
678A THR* 3.3 26.7 + - - +
697A TYR* 3.3 19.4 + - - -
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Residues in contact with MET 675 (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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669A GLN 4.5 5.8 - - - +
670A LEU* 3.4 37.7 - - + -
672A SER* 3.0 24.2 + - - +
674A GLY* 1.3 75.2 - - - +
676A THR* 1.3 62.5 + - - +
678A THR* 2.7 24.5 + - - -
679A VAL* 3.1 16.2 - - - +
693A LEU* 3.8 28.5 - - + +
694A VAL* 4.1 28.7 - - + -
697A TYR* 3.4 41.3 + - + -
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Residues in contact with THR 676 (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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662A GLY* 3.1 32.0 - - - +
664A THR* 2.8 25.8 + - + +
670A LEU 3.7 1.1 + - - -
671A GLU 3.6 13.0 + - - -
672A SER 2.7 22.5 + - - -
673A GLY* 4.0 6.5 - - - -
674A GLY 3.4 0.2 - - - -
675A MET* 1.3 73.8 - - - +
677A ALA* 1.3 60.1 + - - +
679A VAL* 3.3 7.4 + - - +
680A ARG* 3.2 27.1 + - - +
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Residues in contact with ALA 677 (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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673A GLY 3.4 10.3 + - - +
674A GLY* 3.4 11.8 + - - +
675A MET 3.3 0.4 - - - -
676A THR* 1.3 79.7 - - - +
678A THR* 1.3 58.2 + - + +
680A ARG* 3.2 16.3 + - - +
681A GLY* 3.0 23.7 + - - -
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Residues in contact with THR 678 (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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674A GLY 3.3 11.2 + - - +
675A MET* 2.7 37.8 + - - -
677A ALA* 1.3 75.8 - - + +
679A VAL* 1.3 58.5 + - - +
681A GLY* 3.7 2.7 - - - +
682A LEU* 3.0 29.6 + - - +
693A LEU* 4.3 15.4 - - - +
697A TYR* 4.0 17.4 - - + -
702A MET* 5.6 4.3 - - + -
705A ILE* 4.9 15.0 - - + -
709A ILE* 4.6 6.0 - - - +
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Residues in contact with VAL 679 (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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659A LEU* 3.1 39.2 - - + +
660A SER* 4.3 0.2 - - - -
662A GLY* 5.5 0.2 - - - -
664A THR* 4.8 6.5 - - + -
670A LEU* 3.8 26.5 - - + -
675A MET* 3.1 17.3 - - + +
676A THR* 3.3 9.8 + - - +
677A ALA 3.2 0.8 - - - -
678A THR* 1.3 74.7 + - - +
680A ARG* 1.3 64.0 + - - +
682A LEU* 4.5 1.8 - - - +
683A LYS* 3.3 17.8 + - - -
684A PRO* 3.6 15.4 - - + +
690A ILE* 6.5 0.4 - - + -
693A LEU* 3.4 26.2 - - + -
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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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659A LEU 4.3 1.3 + - - -
660A SER 3.5 12.1 - - - +
661A ARG* 2.9 26.5 + - - +
662A GLY* 3.8 19.2 + - - -
663A GLU* 5.8 0.4 - - - +
676A THR* 3.2 17.2 + - - +
677A ALA* 3.2 15.8 + - - +
679A VAL* 1.3 78.1 - - - +
681A GLY* 1.3 56.8 + - - +
683A LYS* 2.9 46.8 + - - +
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Residues in contact with GLY 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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677A ALA 3.0 14.1 + - - -
678A THR* 3.4 5.3 + - - -
679A VAL 3.3 0.2 - - - -
680A ARG* 1.3 78.1 - - - +
682A LEU* 1.3 59.2 + - - +
683A LYS* 4.8 0.7 - - - +
709A ILE* 3.5 17.7 - - - +
713A HIS* 3.3 18.4 + - - -
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Residues in contact with LEU 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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678A THR 3.0 17.0 + - - +
679A VAL* 4.1 4.5 - - - +
680A ARG 3.3 0.4 - - - -
681A GLY* 1.3 78.1 - - - +
683A LYS* 1.3 72.5 - - - +
684A PRO* 4.4 12.1 - - + -
689A ASP* 4.2 15.0 - - + +
693A LEU* 3.9 39.7 - - + -
708A TYR* 3.7 35.0 - - + -
709A ILE* 3.8 21.5 - - + -
712A HIS* 3.4 26.6 - - + +
713A HIS* 3.8 6.4 + - - -
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Residues in contact with LYS 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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660A SER* 2.8 42.7 + - - +
661A ARG* 5.0 2.1 - - - +
679A VAL 3.3 4.2 + - - -
680A ARG* 2.9 37.3 + - - +
681A GLY 4.8 2.0 - - - +
682A LEU* 1.3 83.0 - - - +
684A PRO* 1.3 73.2 - - - +
685A ARG* 3.8 8.4 + - - +
712A HIS* 3.0 16.3 + - + -
713A HIS* 4.0 18.8 - - + -
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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