Contacts of the helix formed by residues 713 - 721 (chain A) in PDB entry 2IUK
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 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A HIS* 4.8 0.4 - - - -
647A ILE* 3.8 14.9 - - - +
709A VAL 2.6 22.5 + - - -
711A THR 3.3 0.2 - - - -
712A ALA* 1.3 79.8 - - - +
714A ALA* 1.3 72.8 + - - +
716A HIS* 4.2 0.2 - - - +
717A ALA* 3.3 21.8 + - - +
790A LEU* 3.8 21.6 - - - +
858A ILE* 3.5 7.2 - - - +
859A PRO* 3.3 16.6 - - - +
860A ASN 3.3 17.3 - - - -
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Residues in contact with ALA 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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639A ASP* 4.7 7.0 - - - +
643A ILE* 3.6 18.8 - - + -
710A TRP* 3.4 38.7 + - + -
713A SER* 1.3 79.5 + - - +
715A LEU* 1.3 66.1 + - - +
717A ALA* 3.4 3.0 + - - +
718A ALA* 3.1 25.8 + - - +
858A ILE* 3.9 13.7 - - + -
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Residues in contact with LEU 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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381A ASN* 3.9 17.7 - - - +
524A SER 4.8 2.5 - - - +
528A ASN* 3.6 23.8 - - + +
529A THR* 3.6 21.8 - - + -
605A GLN* 5.0 9.6 - - + +
636A TYR* 3.7 21.3 - - + +
710A TRP* 2.9 34.6 + - + +
711A THR* 3.5 18.2 - - + +
714A ALA* 1.3 74.0 - - - +
716A HIS* 1.4 64.5 + - - +
718A ALA* 3.4 2.3 + - - +
719A VAL* 3.2 34.1 + - + +
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Residues in contact with HIS 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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525A HIS* 3.5 14.9 + + - -
529A THR* 3.8 13.9 - - + +
530A HIS* 3.5 0.6 + - - -
711A THR 3.3 14.3 + - - +
712A ALA 3.9 5.6 - - - +
713A SER 5.1 0.2 + - - -
714A ALA 3.3 0.2 - - - -
715A LEU* 1.4 77.0 - - - +
717A ALA* 1.3 55.8 + - - +
719A VAL* 3.3 3.4 + - - +
720A ASN* 2.7 56.9 + - + +
721A PHE* 4.3 8.3 - + - -
859A PRO* 5.3 0.2 - - - +
861A SER 3.9 6.1 + - - -
862A ILE* 3.6 41.9 - - + +
863A SER* 4.1 1.6 - - - -
864A ILE* 2.7 22.8 + - + -
901A FE 2.3 28.0 - - - -
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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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713A SER 3.3 18.6 + - - +
714A ALA 3.4 6.1 - - - +
716A HIS* 1.3 75.0 + - - +
718A ALA* 1.3 60.4 + - - +
721A PHE* 2.9 47.6 + - + +
844A LEU* 4.1 8.1 - - - +
857A GLY 3.7 20.6 - - - +
858A ILE* 3.9 20.2 - - + -
859A PRO* 4.3 1.1 - - + -
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Residues in contact with ALA 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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377A GLY 4.3 5.4 - - - +
378A VAL* 3.8 9.5 - - - +
380A PRO* 4.4 3.3 - - + +
636A TYR* 3.9 31.9 - - + -
639A ASP* 4.1 6.7 - - - +
714A ALA 3.1 13.3 + - - +
715A LEU 3.6 4.7 - - - +
717A ALA* 1.3 79.7 - - - +
719A VAL* 1.3 62.5 + - + +
721A PHE 4.9 0.2 - - - -
722A GLY 4.9 1.2 + - - -
842A TYR* 4.1 9.1 + - - +
844A LEU* 4.0 26.7 + - - +
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Residues in contact with VAL 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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378A VAL* 3.7 14.3 - - - +
380A PRO* 4.1 15.0 - - + -
381A ASN* 4.8 3.6 - - - +
520A HIS* 2.8 38.1 + - + +
524A SER* 3.8 29.4 - - - +
525A HIS* 4.2 16.3 - - + -
529A THR* 4.4 2.5 - - + -
636A TYR* 5.8 0.7 - - + -
715A LEU* 3.2 32.3 + - + +
716A HIS* 3.5 13.0 - - - +
718A ALA* 1.3 80.6 - - + +
720A ASN* 1.3 59.1 + - - +
722A GLY 5.0 1.3 - - - -
723A GLN* 3.7 4.8 - - - +
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Residues in contact with ASN 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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525A HIS* 3.2 4.5 + - - +
716A HIS* 2.7 35.8 + - + +
719A VAL* 1.3 74.6 - - - +
721A PHE* 1.3 80.3 + - + +
722A GLY 3.2 2.2 - - - -
723A GLN* 3.1 40.3 + - - +
780A LEU* 2.6 28.1 + - - +
781A SER* 3.6 2.9 + - - -
864A ILE* 3.4 18.1 - - - +
901A FE 3.0 21.8 - - - -
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Residues in contact with PHE 721 (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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716A HIS* 4.3 7.0 - + - -
717A ALA* 2.9 34.2 + - - +
720A ASN* 1.3 93.9 - - - +
722A GLY* 1.3 58.2 + - - +
723A GLN 3.3 1.0 + - - -
725A PRO* 3.8 17.2 - - - +
781A SER* 3.5 25.3 + - - +
782A ARG* 4.1 16.1 + - - -
783A HIS* 3.3 34.3 - + + -
787A GLU* 4.5 1.6 - - - -
844A LEU* 3.7 17.2 - - + +
855A PHE* 4.2 6.2 + - - +
856A LYS 4.8 5.2 - - - +
857A GLY 3.8 10.8 - - - +
859A PRO* 3.5 31.9 - - + -
863A SER* 5.0 0.2 - - - -
864A ILE* 4.0 12.3 - - + -
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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