Contacts of the helix formed by residues 701 - 717 (chain A) in PDB entry 1TAQ
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 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A ASP* 3.6 6.1 - - - +
626A GLU* 5.8 1.1 - - - +
627A ASN* 4.8 5.2 - - - +
697A PHE 3.3 13.5 - - - +
698A GLN* 3.9 9.9 - - - +
699A SER 3.6 6.3 - - - +
700A PHE* 1.4 86.0 - - - +
702A LYS* 1.3 66.9 + - + +
704A ARG* 3.1 14.3 + - + +
705A ALA* 2.9 27.0 + - - +
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Residues in contact with LYS 702 (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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623A SER* 3.8 17.4 - - - +
624A GLY* 3.8 8.7 + - - -
625A ASP* 3.5 26.0 + - + +
626A GLU* 3.2 39.8 + - - +
700A PHE 3.4 0.4 - - - -
701A PRO* 1.3 78.7 - - + +
703A VAL* 1.3 56.4 + - - +
704A ARG 3.2 0.2 - - - -
705A ALA* 3.7 10.5 - - + +
706A TRP* 2.8 35.5 + - - +
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Residues in contact with VAL 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A LEU* 4.5 14.1 - - + -
623A SER* 3.9 15.9 - - - +
625A ASP* 4.1 2.7 - - + -
628A LEU* 3.2 34.8 - - + -
669A VAL* 3.8 19.7 - - + -
696A TYR* 4.1 5.4 - - + +
697A PHE* 3.3 21.1 - - + -
700A PHE* 3.3 22.3 + - + +
701A PRO 3.2 0.4 - - - -
702A LYS* 1.3 76.7 - - - +
704A ARG* 1.3 61.4 + - - +
706A TRP* 3.4 4.0 + - - +
707A ILE* 3.2 26.4 + - + +
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Residues in contact with ARG 704 (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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693A ILE* 6.1 0.2 - - - +
694A GLU* 3.2 38.6 + - - +
697A PHE* 3.5 70.4 + - + +
698A GLN* 5.0 6.1 - - - +
700A PHE 3.5 2.0 + - - -
701A PRO* 3.1 12.9 + - - +
703A VAL* 1.3 77.5 - - - +
705A ALA* 1.3 65.3 + - - +
707A ILE* 3.3 6.2 + - - +
708A GLU* 3.0 47.7 + - + +
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Residues in contact with ALA 705 (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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701A PRO 2.9 16.1 + - - +
702A LYS* 3.7 15.5 - - + +
704A ARG* 1.3 77.2 - - - +
706A TRP* 1.3 62.8 + - - +
708A GLU* 3.3 15.1 + - - +
709A LYS* 3.0 25.5 + - - +
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Residues in contact with TRP 706 (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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619A LEU* 3.9 22.9 - - + -
622A LEU* 3.2 50.6 + - + +
623A SER* 3.8 12.8 - - - +
669A VAL 5.9 2.0 - - - -
670A LEU 5.8 0.7 - - - -
702A LYS 2.8 19.9 + - - +
703A VAL 3.4 4.3 - - - +
705A ALA* 1.3 73.5 - - - +
707A ILE* 1.3 88.8 + - + +
709A LYS* 3.1 6.9 + - + +
710A THR* 2.6 44.4 + - + -
749A PHE* 3.5 35.7 - + + -
752A PRO* 4.1 16.6 - - + -
753A VAL* 3.7 20.9 - - + -
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Residues in contact with ILE 707 (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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619A LEU* 6.2 0.2 - - + -
669A VAL* 4.2 21.3 - - + +
672A GLY* 5.9 2.7 - - - -
697A PHE* 3.9 25.8 - - + -
703A VAL* 3.2 17.9 + - + +
704A ARG* 3.6 5.8 - - - +
706A TRP* 1.3 97.7 - - + +
708A GLU* 1.3 68.0 + - + +
710A THR* 3.2 5.1 + - - -
711A LEU* 3.1 30.5 + - + +
749A PHE* 3.8 29.2 - - + -
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Residues in contact with GLU 708 (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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704A ARG* 3.0 42.7 + - + +
705A ALA* 3.5 15.2 - - - +
707A ILE* 1.3 81.2 - - + +
709A LYS* 1.3 58.7 + - - +
711A LEU* 3.6 7.4 + - - +
712A GLU* 3.3 17.2 + - - +
715A ARG* 4.2 5.6 + - - +
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Residues in contact with LYS 709 (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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705A ALA 3.0 16.5 + - - +
706A TRP* 3.8 4.3 - - + +
708A GLU* 1.3 72.1 - - - +
710A THR* 1.3 56.8 + - - +
711A LEU 3.2 1.8 - - - -
712A GLU* 2.9 36.2 + - - +
713A GLU* 2.8 62.2 + - + +
716A ARG* 4.6 7.7 - - - +
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Residues in contact with THR 710 (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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706A TRP* 2.6 48.1 + - + -
707A ILE* 3.5 8.1 - - - -
709A LYS* 1.3 72.3 - - - +
711A LEU* 1.3 60.0 + - + +
713A GLU* 4.2 6.0 - - - +
714A GLY* 2.8 26.5 + - - -
720A VAL* 4.2 10.1 - - + +
748A ALA 4.2 7.9 - - - +
749A PHE* 3.7 31.4 - - + +
752A PRO* 4.3 11.4 - - + -
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Residues in contact with LEU 711 (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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707A ILE* 3.1 20.5 + - + +
708A GLU* 3.9 3.4 - - - +
710A THR* 1.3 77.2 - - - +
712A GLU* 1.3 59.8 + - - +
714A GLY 3.7 0.2 - - - -
715A ARG* 2.8 55.7 + - - +
733A LEU* 3.7 10.9 - - + +
745A GLU* 3.7 35.2 - - + +
748A ALA* 3.7 23.8 - - + -
749A PHE* 3.7 30.7 - - + +
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Residues in contact with GLU 712 (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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708A GLU 3.3 13.4 + - - +
709A LYS* 2.9 44.0 + - - +
711A LEU* 1.3 75.4 - - - +
713A GLU* 1.3 60.3 + - - +
715A ARG* 3.2 12.3 + - + +
716A ARG* 2.8 45.8 + - + +
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Residues in contact with GLU 713 (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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709A LYS* 2.8 40.4 + - - +
710A THR* 4.2 4.4 - - - +
712A GLU* 1.3 74.3 - - - +
714A GLY* 1.3 57.4 + - - +
716A ARG* 3.7 28.5 + - - +
717A ARG* 2.7 70.3 + - - +
719A TYR 4.3 0.9 - - - -
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Residues in contact with GLY 714 (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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710A THR 2.8 19.9 + - - -
712A GLU 3.1 0.2 - - - -
713A GLU* 1.3 77.5 - - - +
715A ARG* 1.3 54.1 + - - +
718A GLY* 2.8 34.7 + - - -
719A TYR 3.5 15.4 + - - -
720A VAL* 4.2 8.5 - - - +
730A VAL* 4.6 1.8 - - - +
733A LEU* 3.5 18.2 - - - +
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Residues in contact with ARG 715 (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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708A GLU* 4.2 6.3 + - - +
711A LEU* 2.8 54.7 + - - +
712A GLU* 3.7 11.7 - - + +
714A GLY* 1.3 75.5 - - - +
716A ARG* 1.3 63.5 + - - +
718A GLY* 4.0 3.8 + - - -
733A LEU* 3.4 28.9 + - + +
734A GLU* 4.3 26.6 - - - +
741A ARG* 4.2 22.1 - - - +
745A GLU* 3.0 27.7 + - - +
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Residues in contact with ARG 716 (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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709A LYS* 4.6 12.1 - - - +
712A GLU* 2.8 32.5 + - + +
713A GLU* 3.7 27.6 + - - +
715A ARG* 1.3 75.6 - - - +
717A ARG* 1.3 89.9 + - - +
718A GLY* 3.6 0.3 + - - -
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Residues in contact with ARG 717 (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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713A GLU* 2.7 56.5 + - - +
716A ARG* 1.3 105.6 - - - +
718A GLY* 1.3 55.9 + - - +
719A TYR* 3.2 67.5 + - + +
720A VAL* 5.3 2.2 - - - +
721A GLU* 3.8 26.1 + - - +
729A TYR* 5.6 0.9 - - - -
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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