Contacts of the helix formed by residues 709 - 725 (chain A) in PDB entry 1Q2L
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 THR 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A ILE* 3.2 24.7 - - + -
515A LYS 3.8 19.5 - - - +
536A TYR* 3.7 5.2 - - - -
708A MET* 1.3 76.0 - - - +
710A GLU* 1.3 69.7 - - - +
711A ALA* 3.5 8.1 + - - +
712A GLN* 3.0 34.6 + - - +
713A ALA* 2.9 22.7 + - - +
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Residues in contact with GLU 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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515A LYS 4.7 0.7 - - - +
516A SER* 3.8 3.6 - - - -
517A GLU* 3.1 57.6 + - - +
520A TYR* 2.5 36.3 + - - +
526A ILE* 4.4 19.7 - - + -
536A TYR* 3.4 27.6 + - + -
709A THR* 1.3 78.1 - - - +
711A ALA* 1.3 59.6 + - - +
713A ALA* 3.4 4.0 + - - +
714A THR* 2.9 35.8 + - - +
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Residues in contact with ALA 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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517A GLU* 5.0 0.6 + - - -
709A THR* 3.2 7.9 + - - +
710A GLU* 1.3 77.5 - - - +
712A GLN* 1.3 65.2 + - + +
714A THR* 3.0 7.1 + - - -
715A THR* 3.0 33.9 + - + +
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Residues in contact with GLN 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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514A ILE* 3.5 20.4 - - - +
610A THR* 5.2 2.0 + - - -
614A PRO* 5.9 2.1 - - + +
707A ASN 4.4 0.2 + - - -
708A MET* 3.4 26.4 - - + +
709A THR* 3.0 40.6 + - - +
711A ALA* 1.3 76.5 - - - +
713A ALA* 1.3 63.7 + - - +
715A THR* 2.9 21.2 + - - -
716A LEU* 3.0 14.0 + - - +
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Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.6 10.5 - - + +
536A TYR* 4.0 22.0 - - + -
704A VAL* 4.1 26.5 - - + +
708A MET* 4.0 11.6 - - + +
709A THR 2.9 16.4 + - - +
710A GLU* 3.6 4.9 - - - +
712A GLN* 1.3 77.8 - - - +
714A THR* 1.3 61.9 + - + +
716A LEU* 3.5 3.0 + - - +
717A ALA* 3.1 22.2 + - - +
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Residues in contact with THR 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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526A ILE* 4.2 17.0 - - + -
527A VAL* 3.6 29.8 - - + -
534A VAL* 4.8 5.4 - - + -
710A GLU 2.9 18.9 + - - +
711A ALA* 3.0 14.1 + - - -
713A ALA* 1.3 74.6 - - + +
715A THR* 1.3 65.2 + - - +
717A ALA* 3.3 8.2 + - - +
718A ARG* 2.9 39.4 + - - +
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Residues in contact with THR 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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711A ALA* 3.0 23.0 + - + +
712A GLN* 2.9 23.4 + - - -
714A THR* 1.3 77.2 - - - +
716A LEU* 1.3 59.8 + - - +
718A ARG* 3.9 5.1 - - - +
719A ASP* 2.8 44.2 + - - +
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Residues in contact with LEU 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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550A VAL* 4.2 30.1 - - + -
613A LEU* 5.4 0.7 - - + +
614A PRO* 3.8 40.8 - - + +
617A PHE* 4.3 11.4 - - + -
618A GLN* 4.0 17.3 - - + +
702A PHE* 5.4 3.4 - - + -
704A VAL* 5.4 3.1 - - + -
708A MET* 4.0 21.3 - - + -
712A GLN 3.0 17.4 + - - +
713A ALA 3.8 5.2 - - - +
715A THR* 1.3 76.6 + - - +
717A ALA* 1.3 58.9 + - - +
719A ASP* 3.3 5.3 + - - +
720A VAL* 2.9 44.0 + - + +
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Residues in contact with ALA 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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532A LEU* 4.5 5.3 - - + +
534A VAL* 3.4 32.5 - - + -
702A PHE* 3.6 35.4 - - + -
713A ALA 3.1 12.9 + - - +
714A THR 3.4 8.3 - - - +
715A THR 3.2 0.2 - - - -
716A LEU* 1.3 76.8 - - - +
718A ARG* 1.3 58.2 + - - +
720A VAL 3.4 0.9 + - - -
721A GLN* 3.0 27.4 + - - +
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Residues in contact with ARG 718 (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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527A VAL* 4.1 24.2 - - - +
529A GLU* 4.3 16.0 + - - +
531A ASN* 5.9 1.6 - - - +
532A LEU* 3.6 26.9 - - + +
714A THR* 2.9 24.1 + - - +
715A THR* 4.1 5.6 - - - +
717A ALA* 1.3 73.2 - - - +
719A ASP* 1.3 63.1 + - - +
721A GLN* 3.7 11.8 + - - +
722A LYS* 2.9 29.1 + - - +
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Residues in contact with ASP 719 (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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618A GLN* 3.7 30.5 + - - +
715A THR* 2.8 37.4 + - - +
716A LEU* 3.7 5.1 - - - +
718A ARG* 1.3 74.7 - - - +
720A VAL* 1.3 59.1 + - - +
722A LYS* 3.5 26.1 + - - +
723A GLN* 3.0 28.4 + - - +
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Residues in contact with VAL 720 (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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552A LEU* 4.1 10.5 - - + -
617A PHE* 4.1 17.3 - - + -
618A GLN* 4.5 4.7 - - + -
621A LEU* 4.5 7.0 - - + -
700A PRO* 5.9 0.4 - - + -
702A PHE* 3.7 19.7 - - + -
716A LEU* 2.9 38.1 + - + +
717A ALA 3.7 4.7 - - - +
719A ASP* 1.3 76.2 - - - +
721A GLN* 1.3 61.7 + - - +
723A GLN* 3.2 15.0 + - - +
724A LEU* 2.9 51.2 + - + +
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Residues in contact with GLN 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ASN* 2.7 43.0 + - - +
532A LEU* 3.4 28.2 - - + +
700A PRO* 3.7 18.8 - - + +
717A ALA 3.0 16.5 + - - +
718A ARG* 3.7 12.3 + - - +
720A VAL* 1.3 77.5 - - - +
722A LYS* 1.3 53.4 + - - +
724A LEU* 4.8 2.2 - - - -
725A GLY* 2.8 33.1 + - - -
726A ALA 3.2 25.8 + - - +
727A ASP* 4.6 0.6 - - - +
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Residues in contact with LYS 722 (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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618A GLN* 5.4 2.7 + - - -
718A ARG 2.9 18.4 + - - +
719A ASP* 3.5 30.7 + - - +
721A GLN* 1.3 78.6 - - - +
723A GLN* 1.3 68.5 + - - +
725A GLY* 3.2 12.5 + - - -
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Residues in contact with GLN 723 (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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618A GLN* 2.7 58.9 + - - +
621A LEU* 4.5 8.5 - - - +
622A GLU* 3.2 28.4 + - + +
695A LYS* 5.4 1.9 + - - -
719A ASP 3.0 14.0 + - - +
720A VAL* 3.4 15.2 + - - +
722A LYS* 1.3 85.3 - - - +
724A LEU* 1.3 64.6 + - + +
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Residues in contact with LEU 724 (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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552A LEU* 4.4 0.4 - - + -
554A LEU* 3.9 36.3 - - + -
621A LEU* 4.2 20.6 - - + +
625A PHE* 3.7 31.6 - - + -
695A LYS* 3.2 41.6 + - + +
700A PRO* 5.4 1.1 - - + -
720A VAL* 2.9 39.5 + - + +
721A GLN* 5.2 0.9 - - - -
723A GLN* 1.3 82.5 - - + +
725A GLY* 1.3 65.4 + - - +
726A ALA* 3.2 13.9 + - + +
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Residues in contact with GLY 725 (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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695A LYS 4.8 1.1 - - - +
696A SER* 5.3 3.5 - - - -
697A GLY 5.5 0.2 + - - -
721A GLN* 2.8 15.7 + - - -
722A LYS* 3.2 10.7 + - - -
724A LEU* 1.3 74.7 - - - +
726A ALA* 1.3 62.8 + - - +
727A ASP* 3.3 6.5 + - - +
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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