Contacts of the helix formed by residues 306 - 316 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305R THR* 1.3 94.3 + - - +
307R ARG* 1.3 66.8 + - - +
308R LEU* 3.6 8.1 + - - +
309R ASN* 2.9 36.3 + - - +
310R LYS* 3.2 20.6 + - - +
499R ASP* 4.8 1.1 - - - -
617R ILE* 5.5 7.6 - - + -
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Residues in contact with ARG 307 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306R THR* 1.3 76.6 - - - +
308R LEU* 1.3 84.7 + - - +
310R LYS* 3.6 2.1 + - - +
311R GLU* 3.0 26.3 + - - +
499R ASP* 3.6 23.3 + - - +
514R PHE* 3.1 41.7 + - + +
515R VAL* 3.9 0.4 - - - +
516R GLY 3.9 20.6 - - - +
556R ASP* 5.0 9.3 + - - -
557R THR* 4.3 12.3 - - - +
560R ALA* 3.7 25.9 - - - +
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Residues in contact with LEU 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306R THR* 3.0 7.2 + - - +
307R ARG* 1.3 116.0 - - - +
309R ASN* 1.3 66.4 + - - +
310R LYS 3.1 1.3 - - - -
311R GLU* 3.4 17.7 - - + +
312R GLU* 3.0 37.3 + - + +
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Residues in contact with ASN 309 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303R HIS* 3.4 11.4 + - - +
304R HIS* 3.2 19.4 + - - +
305R THR* 3.1 31.3 + - - +
306R THR* 2.9 30.2 + - - +
308R LEU* 1.3 78.3 - - - +
310R LYS* 1.3 63.1 + - - +
312R GLU* 3.7 20.9 + - - +
313R LYS* 3.8 21.5 - - - +
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Residues in contact with LYS 310 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304R HIS* 4.2 22.0 - - + +
305R THR 4.9 6.7 + - - +
306R THR 3.4 15.0 - - - +
307R ARG* 3.7 3.4 - - - +
308R LEU 3.1 0.2 - - - -
309R ASN* 1.3 75.9 - - - +
311R GLU* 1.3 67.2 + - - +
313R LYS* 3.1 20.8 + - - +
314R VAL* 3.3 13.4 + - - +
449R ILE* 5.3 4.3 - - + -
496R PHE* 3.0 44.4 + - + +
497R LEU* 3.2 24.4 + - - +
499R ASP* 2.6 34.5 + - + +
514R PHE* 3.3 23.8 - - + -
631R LYS* 4.6 1.8 - - - +
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Residues in contact with GLU 311 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307R ARG* 3.0 13.8 + - - +
308R LEU* 3.4 23.1 - - + +
310R LYS* 1.3 79.9 - - - +
312R GLU* 1.3 67.3 + - + +
314R VAL* 3.3 1.5 + - - +
315R LYS* 2.9 49.6 + - + +
512R ALA 4.2 2.9 - - - +
513R ILE* 3.2 30.1 - - - +
514R PHE* 2.7 42.4 + - + +
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Residues in contact with GLU 312 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308R LEU* 3.0 27.0 + - + +
309R ASN* 3.8 12.6 - - - +
310R LYS 3.1 0.2 + - - -
311R GLU* 1.3 79.3 - - + +
313R LYS* 1.3 65.8 + - + +
315R LYS* 3.3 14.3 + - - +
316R GLU* 3.7 13.5 - - - +
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Residues in contact with LYS 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299R ALA 2.8 19.6 + - - -
300R TYR* 2.8 66.4 + - + +
303R HIS 3.4 15.0 + - - -
304R HIS* 3.8 8.4 + - - +
309R ASN* 3.8 27.1 + - - +
310R LYS* 3.1 7.0 + - - +
312R GLU* 1.3 77.2 - - + +
314R VAL* 1.3 63.5 + - + +
316R GLU* 3.4 12.9 + - - +
317R TRP* 3.3 22.7 + - - -
447R ARG* 5.0 0.2 + - - -
449R ILE* 3.9 16.2 - - + -
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Residues in contact with VAL 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310R LYS 3.3 7.6 + - - +
311R GLU* 4.0 2.2 - - - +
313R LYS* 1.3 74.4 - - + +
315R LYS* 1.3 65.9 + - - +
317R TRP* 3.1 32.3 + - + +
320R CYS* 4.0 12.6 - - - -
449R ILE* 3.8 28.5 - - + -
456R MET* 4.7 0.4 - - - -
501R LEU* 3.9 30.1 - - + -
509R PRO* 3.2 24.3 - - + +
514R PHE* 3.9 19.1 - - + -
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Residues in contact with LYS 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311R GLU* 2.9 45.7 + - + +
312R GLU* 3.6 7.9 - - - +
313R LYS 3.3 0.4 - - - -
314R VAL* 1.3 76.4 - - - +
316R GLU* 1.3 60.3 + - + +
317R TRP 3.1 6.1 + - - +
509R PRO 3.3 13.0 - - - +
510R GLY* 3.3 38.7 + - - +
511R SER* 5.1 2.0 - - - +
512R ALA 2.9 25.7 + - - +
513R ILE* 4.3 6.3 - - - +
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Residues in contact with GLU 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300R TYR* 5.9 2.3 - - - -
312R GLU 3.7 15.0 - - - +
313R LYS* 3.4 9.9 + - - +
314R VAL 3.2 1.4 - - - -
315R LYS* 1.3 77.7 - - + +
317R TRP* 1.3 66.9 + - + +
318R SER* 5.2 0.3 + - - -
447R ARG* 4.2 15.5 + - - +
460R THR* 4.6 11.8 - - - +
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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