Contacts of the helix formed by residues 306 - 316 (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 THR 306 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q THR* 1.3 93.8 + - - +
307Q ARG* 1.3 66.9 + - - +
308Q LEU* 3.6 8.5 + - - +
309Q ASN* 2.9 35.4 + - - +
310Q LYS* 3.2 21.0 + - - +
499Q ASP* 4.8 0.9 - - - -
617Q ILE* 5.5 8.1 - - + -
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Residues in contact with ARG 307 (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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306Q THR* 1.3 75.7 - - - +
308Q LEU* 1.3 86.3 + - - +
310Q LYS* 3.6 1.9 + - - +
311Q GLU* 3.0 27.0 + - - +
499Q ASP* 3.6 22.8 + - - +
514Q PHE* 3.1 41.8 + - + +
515Q VAL* 3.9 0.4 - - - +
516Q GLY 3.9 21.3 - - - +
556Q ASP 5.0 9.6 + - - -
557Q THR* 4.3 12.3 - - - +
560Q ALA* 3.7 25.5 - - - +
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Residues in contact with LEU 308 (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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306Q THR* 3.0 7.9 + - - +
307Q ARG* 1.3 118.0 - - - +
309Q ASN* 1.3 65.3 + - - +
310Q LYS 3.1 2.2 - - - -
311Q GLU* 3.5 17.6 - - + +
312Q GLU* 3.0 38.2 + - + +
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Residues in contact with ASN 309 (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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303Q HIS* 3.4 11.5 + - - +
304Q HIS* 3.2 19.6 + - - +
305Q THR* 3.1 30.6 + - - +
306Q THR* 2.9 31.2 + - - +
308Q LEU* 1.3 79.2 - - - +
310Q LYS* 1.3 63.8 + - - +
312Q GLU* 3.7 20.9 + - - +
313Q LYS* 3.8 21.5 + - - +
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Residues in contact with LYS 310 (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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304Q HIS* 4.2 22.0 - - + +
305Q THR 4.9 6.9 + - - +
306Q THR 3.2 15.0 + - - +
307Q ARG* 3.7 3.1 - - - +
308Q LEU 3.1 0.2 - - - -
309Q ASN* 1.3 76.7 - - - +
311Q GLU* 1.3 66.9 + - - +
313Q LYS* 3.1 20.9 + - - +
314Q VAL* 3.3 13.0 + - - +
449Q ILE* 5.3 4.0 - - + +
496Q PHE* 3.0 43.9 + - + +
497Q LEU* 3.2 25.0 + - - +
499Q ASP* 2.6 35.3 + - + +
514Q PHE* 3.3 24.2 - - + -
631Q LYS* 4.6 2.0 - - - +
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Residues in contact with GLU 311 (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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307Q ARG* 3.0 15.1 + - - +
308Q LEU* 3.5 21.3 - - + +
310Q LYS* 1.3 78.7 - - - +
312Q GLU* 1.3 68.8 + - + +
314Q VAL* 3.3 1.5 + - - -
315Q LYS* 2.9 49.3 + - + +
501Q LEU* 6.4 0.4 - - + -
512Q ALA 4.2 2.7 - - - +
513Q ILE* 3.2 30.7 - - - +
514Q PHE* 2.7 41.8 + - + +
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Residues in contact with GLU 312 (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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308Q LEU* 3.0 27.3 + - + +
309Q ASN* 3.8 11.3 - - - +
310Q LYS 3.1 0.4 + - - -
311Q GLU* 1.3 78.8 - - + +
313Q LYS* 1.3 65.1 + - + +
315Q LYS* 3.3 14.4 + - - +
316Q GLU* 3.7 14.2 - - - +
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Residues in contact with LYS 313 (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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299Q ALA* 2.8 19.6 + - - +
300Q TYR* 2.8 66.9 + - + +
303Q HIS 3.4 14.6 + - - -
304Q HIS* 3.8 7.8 + - - +
309Q ASN* 3.8 25.5 + - - +
310Q LYS* 3.1 7.0 + - - +
312Q GLU* 1.3 77.3 - - + +
314Q VAL* 1.3 62.6 + - - +
316Q GLU* 3.4 14.1 + - - +
317Q TRP* 3.3 22.1 + - - -
447Q ARG* 5.0 0.2 + - - -
449Q ILE* 3.9 16.8 - - + -
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Residues in contact with VAL 314 (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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310Q LYS 3.3 7.8 + - - +
311Q GLU* 4.0 2.2 - - - +
313Q LYS* 1.3 74.5 - - + +
315Q LYS* 1.3 64.7 + - + +
317Q TRP* 3.1 31.9 + - + +
320Q CYS* 4.0 12.1 - - - -
449Q ILE* 3.8 28.9 - - + -
456Q MET* 4.7 0.2 - - - -
501Q LEU* 3.9 30.1 - - + -
509Q PRO* 3.2 24.0 - - + +
514Q PHE* 3.9 20.6 - - + -
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Residues in contact with LYS 315 (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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311Q GLU* 2.9 45.7 + - + +
312Q GLU* 3.6 6.5 - - - +
313Q LYS 3.3 0.4 - - - -
314Q VAL* 1.3 76.4 - - + +
316Q GLU* 1.3 59.8 + - + +
317Q TRP 3.1 6.3 + - - +
509Q PRO 3.3 12.3 - - - +
510Q GLY* 3.3 38.6 + - - +
511Q SER* 5.1 1.8 - - - +
512Q ALA 2.9 25.8 + - - +
513Q ILE* 4.3 6.7 - - - +
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Residues in contact with GLU 316 (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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300Q TYR* 5.9 1.9 - - - -
312Q GLU 3.7 15.0 - - - +
313Q LYS* 3.4 9.2 + - - +
314Q VAL 3.2 1.2 - - - -
315Q LYS* 1.3 78.6 - - + +
317Q TRP* 1.3 66.5 + - + +
318Q SER* 5.2 0.5 + - - -
447Q ARG* 4.2 15.3 + - - +
460Q THR* 4.6 12.0 - - - +
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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