Contacts of the helix formed by residues 672 - 684 (chain A) in PDB entry 1Q99
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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666A THR* 4.6 0.2 - - - -
670A LYS 3.9 0.6 + - - -
671A PHE* 1.3 77.2 - - - +
673A LYS* 1.3 64.8 + - - +
674A ASP* 3.4 9.1 + - - +
675A GLU* 3.0 27.0 + - - +
676A ALA* 3.0 21.5 + - - +
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Residues in contact with LYS 673 (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 GLU* 4.1 11.0 - - - +
666A THR* 4.2 12.8 - - + +
671A PHE 3.8 0.6 + - - -
672A SER* 1.3 73.3 - - - +
674A ASP* 1.3 60.2 + - - +
676A ALA* 3.6 2.3 + - - +
677A LYS* 2.9 65.2 + - - +
647B ARG 5.9 2.0 - - - +
649B LEU* 6.2 4.5 - - + -
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Residues in contact with ASP 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* 3.1 7.4 + - - +
673A LYS* 1.3 76.9 - - - +
675A GLU* 1.3 60.1 + - - +
677A LYS* 3.0 15.9 + - - +
678A GLU* 2.8 30.4 + - - +
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Residues in contact with GLU 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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267A LEU* 3.6 17.5 - - - +
271A LYS* 5.2 1.4 + - - -
671A PHE* 3.5 28.9 - - + -
672A SER* 3.0 21.5 + - - +
674A ASP* 1.3 74.9 - - - +
676A ALA* 1.3 58.5 + - - +
678A GLU* 3.1 15.5 + - - +
679A ILE* 2.8 38.9 + - + +
705A TRP* 3.0 30.7 + - - -
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Residues in contact with ALA 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 GLU* 3.8 11.1 - - + +
665A LEU* 3.8 28.4 - - + +
666A THR* 3.4 33.9 - - + -
671A PHE* 4.2 5.5 - - + +
672A SER 3.0 10.5 + - - +
673A LYS 3.8 1.1 - - - +
675A GLU* 1.3 76.5 - - - +
677A LYS* 1.3 58.0 + - - +
679A ILE* 4.5 0.7 - - - -
680A SER* 2.8 32.4 + - - -
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Residues in contact with LYS 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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662A GLU* 3.2 32.0 + - - +
673A LYS* 2.9 56.8 + - - +
674A ASP* 3.0 18.6 + - - +
676A ALA* 1.3 73.3 - - - +
678A GLU* 1.3 56.5 + - - +
680A SER* 3.7 2.6 - - - -
681A ASP* 2.7 37.4 + - - +
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Residues in contact with GLU 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 ASP 2.8 13.1 + - - +
675A GLU* 3.6 21.7 - - - +
677A LYS* 1.3 76.5 - - - +
679A ILE* 1.3 62.0 + - - +
681A ASP* 3.1 8.5 + - - +
682A PHE* 2.9 22.3 + - - +
703A HIS* 3.7 8.3 - - + -
704A PRO* 3.6 12.4 - - + +
705A TRP* 3.3 46.0 + - + -
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Residues in contact with ILE 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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267A LEU* 5.1 0.4 - - + -
598A ILE* 4.1 15.5 - - + -
665A LEU* 3.6 23.1 - - + -
671A PHE* 4.0 26.2 - - + -
675A GLU* 2.8 45.8 + - + +
678A GLU* 1.3 71.6 - - - +
680A SER* 1.3 58.5 + - - +
682A PHE* 3.0 10.3 + - + +
683A LEU* 2.8 48.4 + - + +
705A TRP* 3.8 33.7 - - + +
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Residues in contact with SER 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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661A LEU* 3.9 29.8 - - - +
662A GLU* 4.2 17.0 + - - +
665A LEU* 4.4 0.4 - - - +
676A ALA 2.8 19.7 + - - -
677A LYS* 3.9 3.8 - - - -
679A ILE* 1.3 77.3 - - - +
681A ASP* 1.3 57.1 + - - +
684A SER* 2.6 50.6 + - - -
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Residues in contact with ASP 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 LYS 2.7 22.6 + - - +
678A GLU* 3.3 10.5 - - - +
680A SER* 1.3 73.2 - - - +
682A PHE* 1.3 57.2 + - - +
684A SER* 4.9 0.9 - - - -
685A PRO* 3.0 26.0 - - - +
703A HIS* 2.5 21.2 + - + +
704A PRO* 5.8 0.2 - - - +
723A TYR* 2.4 38.0 + - - -
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Residues in contact with PHE 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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274A SER* 4.5 1.3 - - - -
278A LEU* 3.9 10.5 - - + -
594A ILE* 3.9 17.0 - - + -
678A GLU 2.9 11.7 + - - +
679A ILE* 3.0 10.5 + - + +
681A ASP* 1.3 79.0 - - - +
683A LEU* 1.3 79.0 + - + +
685A PRO* 3.4 8.5 - - - +
686A MET* 3.4 33.1 - - + +
700A LEU* 3.7 23.6 - - + +
703A HIS* 3.6 32.8 - + + -
705A TRP* 3.5 36.1 - + + -
706A LEU* 3.8 35.4 - - + -
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Residues in contact with LEU 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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591A ALA* 4.2 10.5 - - + +
594A ILE* 4.0 19.7 - - + -
595A PHE* 4.5 25.1 - - + -
598A ILE* 4.5 8.7 - - + -
603A LEU* 6.4 0.4 - - + -
661A LEU* 4.0 20.0 - - + -
679A ILE* 2.8 40.0 + - + +
682A PHE* 1.3 80.3 - - + +
684A SER* 1.3 60.3 + - - +
685A PRO 3.3 2.2 - - - -
686A MET* 2.8 49.4 + - + +
687A LEU* 3.0 19.3 + - + +
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Residues in contact with SER 684 (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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626A LEU* 5.6 7.1 - - - +
661A LEU* 4.2 7.4 - - - +
680A SER* 2.6 45.3 + - - -
681A ASP* 4.9 1.1 - - - -
683A LEU* 1.3 71.9 - - - +
685A PRO* 1.3 67.1 - - - +
687A LEU* 2.9 22.4 + - - +
688A GLN* 3.3 10.7 + - - +
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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