Contacts of the helix formed by residues 333 - 347 (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 PRO 333 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109Q ARG* 3.7 23.1 - - - +
331Q PHE 2.9 6.2 - - - +
332Q TRP* 1.3 99.0 - - + +
334Q GLY* 1.3 67.1 + - - +
335Q TRP* 3.1 38.6 - - + +
336Q LEU* 2.9 33.7 + - + +
337Q ARG 3.6 0.5 + - - -
405Q LEU* 4.0 26.7 - - + -
486Q MET* 4.4 0.4 - - - -
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Residues in contact with GLY 334 (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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105Q ASN* 5.0 4.8 + - - +
106Q LEU* 5.5 4.0 - - - +
109Q ARG* 5.4 0.6 - - - +
332Q TRP* 3.6 7.4 + - - -
333Q PRO* 1.3 71.4 - - - +
335Q TRP* 1.3 63.9 + - - +
337Q ARG* 2.9 36.8 + - - +
338Q ASP* 3.1 10.2 + - - +
388Q GLU* 3.2 26.4 + - - -
390Q GLY* 5.8 1.3 - - - -
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Residues in contact with TRP 335 (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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106Q LEU* 6.2 2.4 - - + +
109Q ARG* 3.9 5.1 - - - +
115Q ALA 3.1 18.6 + - - -
116Q ASP* 3.2 29.2 - - + +
117Q GLY* 3.3 17.7 - - - +
118Q PRO* 3.8 23.6 - - + -
127Q PHE* 3.7 29.8 - + - -
333Q PRO* 3.0 36.0 - - + +
334Q GLY* 1.3 79.3 - - - +
336Q LEU* 1.3 92.5 + - + +
338Q ASP* 3.2 10.4 + - - +
339Q LEU* 2.8 36.0 + - + +
405Q LEU* 5.2 1.6 - - + -
485Q TYR* 3.7 26.2 - + + -
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Residues in contact with LEU 336 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Q PHE* 4.0 25.6 - - + -
332Q TRP* 4.0 14.6 - - + +
333Q PRO* 2.9 21.6 + - + +
335Q TRP* 1.3 96.4 - - + +
337Q ARG* 1.3 58.5 + - - +
339Q LEU* 4.2 8.3 - - + -
340Q ILE* 2.9 55.4 + - + +
404Q LEU* 4.2 7.4 - - + -
405Q LEU* 3.4 50.9 - - + +
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Residues in contact with ARG 337 (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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332Q TRP* 3.8 26.7 - - + -
333Q PRO 3.6 2.2 + - - -
334Q GLY* 2.9 22.4 + - - +
336Q LEU* 1.3 79.8 - - - +
338Q ASP* 1.3 90.9 + - - +
340Q ILE* 3.4 5.7 + - - +
341Q CYS* 2.9 38.5 + - - -
357Q PHE* 5.3 1.9 - - + -
358Q GLU* 3.7 15.3 - - - +
361Q LEU* 3.1 50.2 + - + -
362Q LYS* 3.8 23.1 - - - +
387Q LEU 4.0 0.8 + - - -
388Q GLU* 2.8 39.1 + - - +
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Residues in contact with ASP 338 (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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334Q GLY 3.1 7.2 + - - +
335Q TRP* 3.7 9.3 - - - +
337Q ARG* 1.3 112.5 + - - +
339Q LEU* 1.3 58.9 + - - +
341Q CYS* 3.4 7.2 + - - +
342Q ASP* 2.9 30.0 + - - +
358Q GLU* 4.4 8.3 - - - +
362Q LYS* 3.9 9.7 + - - -
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Residues in contact with LEU 339 (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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118Q PRO* 3.7 30.7 - - + -
124Q ASN* 3.9 8.5 - - - +
127Q PHE* 3.9 27.4 - - + -
128Q ARG* 3.5 42.6 + - + +
131Q VAL* 4.7 0.9 - - + -
335Q TRP* 2.8 31.1 + - + +
336Q LEU* 3.6 7.0 - - + +
338Q ASP* 1.3 72.4 - - - +
340Q ILE* 1.3 67.7 + - + +
342Q ASP* 3.1 7.3 + - - +
343Q GLU* 2.8 28.1 + - + +
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Residues in contact with ILE 340 (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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131Q VAL* 3.8 28.4 - - + +
135Q PHE* 5.1 4.9 - - + -
332Q TRP* 4.6 1.3 - - + -
336Q LEU* 2.9 52.3 + - + +
337Q ARG* 3.6 4.5 - - - +
339Q LEU* 1.3 76.4 - - + +
341Q CYS* 1.3 62.4 + - - +
343Q GLU* 3.3 1.6 + - - +
344Q LEU* 2.9 42.0 + - + +
357Q PHE* 4.4 14.6 - - + -
401Q MET* 3.9 27.1 - - + -
404Q LEU* 3.9 22.2 - - + -
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Residues in contact with CYS 341 (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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337Q ARG* 2.9 21.9 + - - +
338Q ASP* 3.6 7.4 - - - +
340Q ILE* 1.3 77.0 - - - +
342Q ASP* 1.3 63.4 + - - +
344Q LEU* 3.2 5.8 + - - +
345Q LEU* 3.0 29.9 + - + +
354Q VAL* 3.5 21.5 - - + +
357Q PHE* 4.0 16.6 - - - -
358Q GLU* 3.5 44.6 - - + +
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Residues in contact with ASP 342 (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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128Q ARG* 2.9 32.6 + - - +
338Q ASP 2.9 14.0 + - - +
339Q LEU* 3.5 8.1 - - - +
341Q CYS* 1.3 77.0 - - - +
343Q GLU* 1.3 62.2 + - - +
345Q LEU* 3.1 16.8 + - - +
346Q ASN* 3.0 32.9 + - - +
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Residues in contact with GLU 343 (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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128Q ARG* 2.6 70.2 + - + +
131Q VAL* 3.9 17.9 - - + -
132Q ARG* 2.2 44.0 + - + +
339Q LEU 2.8 19.0 + - - +
340Q ILE 3.8 3.8 - - - +
342Q ASP* 1.3 74.7 - - - +
344Q LEU* 1.3 57.9 + - - +
346Q ASN* 3.2 11.1 + - - +
347Q MET* 2.8 33.4 + - - +
429Q MET* 4.0 4.8 - - - +
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Residues in contact with LEU 344 (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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131Q VAL* 3.9 11.2 - - + -
135Q PHE* 3.6 40.4 - - + -
340Q ILE* 2.9 35.1 + - + +
341Q CYS* 3.5 8.5 - - - +
343Q GLU* 1.3 72.7 - - - +
345Q LEU* 1.3 66.3 + - - +
347Q MET* 3.3 5.1 + - - -
348Q GLY 3.2 5.0 + - - -
349Q TYR* 3.0 54.5 + - + +
353Q TRP* 4.1 24.0 - - + -
354Q VAL* 4.3 7.9 - - + -
357Q PHE* 4.9 6.7 - - + -
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Residues in contact with LEU 345 (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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341Q CYS* 3.0 21.9 + - + +
342Q ASP* 3.1 17.5 + - - +
344Q LEU* 1.3 76.0 - - - +
346Q ASN* 1.3 56.1 + - - +
348Q GLY* 2.7 27.0 + - - -
349Q TYR 3.8 6.6 + - - +
351Q PRO* 3.8 28.7 - - + +
354Q VAL* 3.7 27.4 - - + -
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Residues in contact with ASN 346 (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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128Q ARG* 3.7 2.2 - - - +
132Q ARG* 4.0 15.4 + - - +
342Q ASP* 3.0 37.7 + - - +
343Q GLU* 3.2 26.4 + - - +
345Q LEU* 1.3 78.3 - - - +
347Q MET* 1.3 59.1 + - - +
348Q GLY* 2.8 7.6 + - - -
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Residues in contact with MET 347 (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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131Q VAL* 3.8 22.2 - - - +
132Q ARG* 3.3 66.5 + - + +
135Q PHE* 3.6 34.3 - - + +
136Q SER* 4.2 6.7 - - - +
343Q GLU 2.8 21.4 + - - +
344Q LEU* 3.6 11.4 - - - +
345Q LEU 3.3 0.2 - - - -
346Q ASN* 1.3 70.7 - - - +
348Q GLY* 1.3 57.8 + - - +
349Q TYR* 4.1 8.7 - - + -
663Q PRO* 3.2 21.6 - - + +
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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