Contacts of the helix formed by residues 563 - 580 (chain Q) in PDB entry 1HI0
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 ILE 563 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65Q PHE* 3.3 46.0 - - + -
78Q ASN* 4.0 23.3 - - + +
80Q VAL* 3.4 28.5 - - + -
84Q PHE* 4.3 6.1 - - + -
518Q ILE* 4.4 13.2 - - + -
561Q CYS* 3.3 1.5 - - - -
562Q PRO* 1.3 79.1 - - + +
564Q TYR* 1.3 68.2 + - - +
565Q SER 3.5 1.8 - - - -
566Q ASP* 3.2 13.4 + - + +
567Q VAL* 3.0 36.3 + - + +
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Residues in contact with TYR 564 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518Q ILE* 4.3 10.3 - - + -
521Q MET* 4.0 13.5 - - + -
554Q MET* 3.3 29.3 - - + +
555Q LYS* 3.0 60.9 + - + +
558Q TYR* 3.7 26.2 - - + +
559Q GLY* 3.7 16.8 - - - +
561Q CYS* 3.1 18.6 + - - +
562Q PRO 3.5 1.0 + - - -
563Q ILE* 1.3 78.9 - - - +
565Q SER* 1.3 79.1 + - - +
567Q VAL* 2.8 11.1 + - - +
568Q LEU* 3.1 34.6 + - + +
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Residues in contact with SER 565 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555Q LYS* 5.7 1.0 + - - -
563Q ILE 3.5 0.2 - - - -
564Q TYR* 1.3 87.9 - - - +
566Q ASP* 1.3 67.4 + - - +
568Q LEU* 3.4 8.9 + - - +
569Q GLU* 3.1 34.5 + - - +
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Residues in contact with ASP 566 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Q PHE* 3.6 37.1 - - + -
562Q PRO 4.4 3.5 - - - +
563Q ILE* 3.4 20.9 - - - +
564Q TYR 2.9 0.2 + - - -
565Q SER* 1.3 79.9 - - - +
567Q VAL* 1.3 58.4 + - - +
569Q GLU* 3.2 10.2 + - - +
570Q ALA* 2.8 29.4 + - - +
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Residues in contact with VAL 567 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q LEU* 4.0 21.8 - - + -
84Q PHE* 5.1 0.9 - - + -
518Q ILE* 3.9 21.8 - - + -
521Q MET* 3.6 26.0 - - + -
522Q LEU* 4.1 15.7 - - + -
563Q ILE* 3.0 28.4 + - + +
564Q TYR 2.8 12.8 + - - +
566Q ASP* 1.3 72.6 - - + +
568Q LEU* 1.3 53.2 + - - +
570Q ALA* 2.9 8.2 + - - +
571Q ILE* 2.7 46.7 + - + +
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Residues in contact with LEU 568 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521Q MET* 4.9 4.5 - - + -
525Q GLN* 5.6 0.2 - - - +
551Q TRP* 4.1 13.5 - - + -
554Q MET* 3.8 30.5 - - + -
564Q TYR* 3.1 56.7 + - + +
565Q SER* 3.8 9.4 - - - +
567Q VAL* 1.3 75.9 - - - +
569Q GLU* 1.3 59.1 + - + +
571Q ILE* 3.3 18.2 + - + +
572Q GLU* 2.8 30.1 + - - +
583Q TYR* 5.7 1.3 - - + -
584Q ARG* 5.4 7.2 + - - +
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Residues in contact with GLU 569 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565Q SER* 3.1 23.2 + - - +
566Q ASP* 3.4 11.3 - - - +
568Q LEU* 1.3 75.2 - - + +
570Q ALA* 1.3 65.3 + - - +
572Q GLU* 3.3 8.0 + - + +
573Q ARG* 2.9 26.0 + - - +
584Q ARG* 6.1 2.0 - - - +
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Residues in contact with ALA 570 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q LEU* 3.9 17.7 - - + -
60Q TYR* 3.9 25.8 - - + -
61Q LEU* 4.0 11.0 - - + -
566Q ASP 2.8 17.9 + - - +
567Q VAL 2.9 7.6 + - - +
569Q GLU* 1.3 70.9 - - - +
571Q ILE* 1.3 59.0 + - - +
573Q ARG* 3.3 14.2 + - - +
574Q CYS* 2.9 33.4 + - - -
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Residues in contact with ILE 571 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q PHE* 3.8 7.7 - - + -
57Q LEU* 3.7 26.2 - - + +
521Q MET* 4.9 3.6 - - + -
522Q LEU* 4.0 10.8 - - + -
525Q GLN* 4.5 9.0 - - - +
526Q PHE* 3.6 29.2 - - + -
567Q VAL* 2.7 29.7 + - + +
568Q LEU* 3.4 17.5 - - + +
570Q ALA* 1.3 70.0 - - - +
572Q GLU* 1.3 68.7 + - - +
573Q ARG 3.0 0.5 + - - -
574Q CYS 3.0 1.6 + - - -
575Q TRP* 2.7 26.9 + - - +
583Q TYR* 3.4 35.7 - - + -
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Residues in contact with GLU 572 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568Q LEU 2.8 20.5 + - - +
569Q GLU* 3.5 8.7 - - + +
571Q ILE* 1.3 75.0 - - - +
573Q ARG* 1.3 57.7 + - - +
575Q TRP* 3.8 1.6 - - - +
576Q TRP* 3.1 39.0 + - + +
582Q SER* 3.0 35.3 + - - -
583Q TYR* 3.1 9.1 + - - +
584Q ARG* 2.9 58.3 + - - +
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Residues in contact with ARG 573 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q GLU* 3.7 21.2 + - - +
60Q TYR* 3.1 55.8 + - - +
569Q GLU 2.9 16.3 + - - +
570Q ALA* 3.3 8.7 - - - +
572Q GLU* 1.3 77.3 - - - +
574Q CYS* 1.3 71.4 + - - +
576Q TRP* 2.8 24.2 + - - +
577Q ASN* 3.1 21.6 + - - +
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Residues in contact with CYS 574 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Q PHE* 3.5 20.7 - - + +
56Q GLU* 3.4 42.4 - - - +
57Q LEU* 3.9 24.0 - - + +
60Q TYR* 5.2 0.7 - - - -
570Q ALA 2.9 22.3 + - - +
573Q ARG* 1.3 86.4 - - - +
575Q TRP* 1.3 61.5 + - - +
577Q ASN* 3.4 5.9 + - - +
578Q ALA* 3.0 28.6 + - - +
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Residues in contact with TRP 575 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600P ARG* 5.6 4.6 - - - +
40Q TYR* 5.5 2.2 - + - -
43Q LEU* 4.4 8.7 - - + -
50Q PHE* 3.9 24.7 - + - -
53Q PHE* 3.5 28.0 - + + -
526Q PHE* 3.9 5.8 - + - -
571Q ILE 2.7 20.3 + - - +
572Q GLU 3.8 4.0 - - - +
574Q CYS* 1.3 71.0 - - - +
576Q TRP* 1.3 61.1 + - - +
578Q ALA 4.4 0.2 - - - +
579Q PHE* 2.8 72.7 + + + +
581Q GLU* 3.4 25.9 - - - +
582Q SER 4.6 0.6 + - - -
583Q TYR* 3.5 51.0 - + + +
586Q TYR* 3.9 32.7 - + - +
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Residues in contact with TRP 576 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572Q GLU* 3.1 28.5 + - + +
573Q ARG* 2.8 13.5 + - - +
575Q TRP* 1.3 78.1 - - - +
577Q ASN* 1.3 63.2 + - - +
580Q GLY* 2.7 61.7 + - - -
581Q GLU* 3.1 33.3 + - - -
582Q SER* 3.6 9.0 - - - +
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Residues in contact with ASN 577 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537P ARG* 5.8 0.3 + - - -
56Q GLU* 3.0 35.7 + - - +
573Q ARG* 3.1 28.2 + - - +
574Q CYS* 3.5 6.1 - - - +
575Q TRP 3.3 0.2 - - - -
576Q TRP* 1.3 78.9 - - - +
578Q ALA* 1.3 62.0 + - - +
580Q GLY 4.8 0.2 + - - -
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Residues in contact with ALA 578 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537P ARG* 4.5 6.7 + - - +
49Q ARG* 3.3 48.3 - - - +
52Q SER* 5.0 4.9 - - - +
53Q PHE* 3.6 17.9 - - + +
56Q GLU* 5.8 0.2 - - - +
574Q CYS 3.0 17.8 + - - +
576Q TRP 3.0 0.2 - - - -
577Q ASN* 1.3 80.2 - - - +
579Q PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 579 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600P ARG* 3.9 21.7 + - - +
43Q LEU* 4.8 13.5 - - + -
47Q ASP* 4.8 0.2 - - - -
49Q ARG* 3.4 50.9 - - + +
50Q PHE* 3.6 32.8 - + + -
53Q PHE* 4.3 5.8 - - + -
575Q TRP* 2.8 71.7 + + - +
578Q ALA* 1.3 85.4 - - + +
580Q GLY* 1.3 65.1 + - - +
581Q GLU* 3.2 18.0 - - + +
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Residues in contact with GLY 580 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576Q TRP* 2.7 52.5 + - - -
577Q ASN 4.6 0.8 + - - -
578Q ALA 3.8 0.2 - - - -
579Q PHE* 1.3 73.4 - - - +
581Q GLU* 1.3 63.9 + - - +
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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