Contacts of the helix formed by residues 428 - 441 (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 ASP 428 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125Q LEU* 3.8 15.1 - - - +
426Q ILE 3.8 0.4 - - - -
427Q LYS* 1.3 88.7 - - - +
429Q MET* 1.3 65.8 + - - +
430Q PRO* 3.0 17.3 - - + +
431Q SER* 2.6 37.7 + - - -
432Q ALA* 2.9 23.2 + - - +
434Q ARG* 4.5 1.7 + - - -
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Residues in contact with MET 429 (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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125Q LEU* 3.5 35.0 - - + +
128Q ARG* 3.7 33.4 - - + +
129Q ALA* 3.8 6.7 - - - +
132Q ARG* 3.2 38.1 - - + +
343Q GLU* 4.0 4.9 - - - +
428Q ASP* 1.3 73.7 - - - +
430Q PRO* 1.3 62.7 - - + +
432Q ALA* 2.9 3.8 + - - +
433Q CYS* 2.6 44.4 + - - -
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Residues in contact with PRO 430 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428Q ASP* 3.0 17.5 - - + +
429Q MET* 1.3 92.0 - - + +
431Q SER* 1.3 64.1 + - - +
433Q CYS* 3.1 6.2 + - + +
434Q ARG* 2.8 45.5 + - - +
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Residues in contact with SER 431 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425Q ARG 3.2 24.3 - - - +
427Q LYS* 2.8 33.2 + - - -
428Q ASP* 2.6 33.4 + - - -
430Q PRO* 1.3 73.1 - - - +
432Q ALA* 1.3 54.2 + - - +
434Q ARG* 3.3 27.2 + - - +
435Q PHE* 2.9 23.4 + - - +
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Residues in contact with ALA 432 (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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125Q LEU* 4.2 12.1 - - + +
126Q LEU* 4.9 3.4 - - + +
129Q ALA* 4.1 16.4 - - + -
426Q ILE* 3.8 24.9 - - + -
428Q ASP 2.9 21.8 + - - +
429Q MET* 3.1 6.7 - - - +
431Q SER* 1.3 73.2 + - - +
433Q CYS* 1.3 68.3 + - - +
435Q PHE* 2.9 5.3 + - - +
436Q LEU* 2.8 24.9 + - - +
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Residues in contact with CYS 433 (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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129Q ALA* 4.0 18.4 - - - +
132Q ARG* 4.2 18.2 - - - -
133Q LEU* 3.9 16.5 - - + +
429Q MET* 2.6 46.5 + - - +
430Q PRO* 3.6 5.6 - - + +
432Q ALA* 1.3 71.9 - - - +
434Q ARG* 1.3 57.6 + - + +
436Q LEU* 3.8 2.1 - - - +
437Q ASP* 2.8 35.1 + - - +
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Residues in contact with ARG 434 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428Q ASP* 4.5 2.0 + - - -
430Q PRO* 2.8 28.1 + - - +
431Q SER* 3.3 46.6 + - - +
433Q CYS* 1.3 78.2 - - + +
435Q PHE* 1.3 63.4 + - - +
437Q ASP* 3.6 5.8 - - - +
438Q SER* 3.0 22.9 + - - -
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Residues in contact with PHE 435 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q LEU* 4.4 7.2 - - + -
411Q LEU* 4.0 31.6 - - + -
415Q LEU* 4.5 11.7 - - + -
422Q LEU* 4.2 19.3 - - + -
425Q ARG* 3.5 35.9 - - + +
426Q ILE* 3.8 33.9 - - + -
431Q SER 2.9 19.2 + - - +
432Q ALA 3.5 2.7 - - - +
434Q ARG* 1.3 76.3 - - - +
436Q LEU* 1.3 56.8 + - - +
438Q SER* 3.0 8.4 + - - -
439Q TYR* 2.8 41.6 + - + +
444Q GLU* 3.9 26.5 - - + -
446Q ILE* 4.7 2.5 - - + -
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Residues in contact with LEU 436 (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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126Q LEU* 3.9 9.6 - - + +
129Q ALA* 3.7 11.7 - - + -
130Q ALA* 3.3 42.6 - - + +
133Q LEU* 3.7 13.5 - - + -
408Q ILE* 3.9 13.7 - - + -
411Q LEU* 4.0 17.0 - - + -
432Q ALA 2.8 17.2 + - - +
433Q CYS 3.8 2.7 - - - +
435Q PHE* 1.3 77.6 - - - +
437Q ASP* 1.3 58.2 + - - +
439Q TYR* 3.1 8.2 + - + +
440Q TRP* 2.8 60.4 + - + +
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Residues in contact with ASP 437 (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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133Q LEU* 3.4 18.0 - - + +
297Q LYS* 3.4 18.7 + - - -
298Q TYR* 2.8 26.0 + - - -
433Q CYS 2.8 19.3 + - - +
434Q ARG* 3.6 7.0 - - - +
436Q LEU* 1.3 78.8 - - - +
438Q SER* 1.3 66.4 + - - +
440Q TRP 3.3 0.5 + - - -
441Q GLN* 2.8 41.2 + - - +
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Residues in contact with SER 438 (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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425Q ARG* 4.7 3.1 + - - -
434Q ARG 3.0 12.8 + - - -
435Q PHE* 3.0 10.4 + - - -
437Q ASP* 1.3 80.4 + - - +
439Q TYR* 1.3 63.4 + - - +
441Q GLN* 3.2 7.8 + - - +
443Q HIS* 3.2 42.9 + - - +
444Q GLU* 2.4 28.0 + - - -
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Residues in contact with TYR 439 (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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301Q THR* 4.1 4.6 - - + +
407Q SER 4.9 0.2 - - - -
410Q TYR 4.8 0.2 - - - -
411Q LEU* 3.7 39.1 + - + -
414Q GLN* 2.7 27.6 + - - -
435Q PHE* 2.8 19.1 + + + +
436Q LEU* 3.4 18.2 - - + +
438Q SER* 1.3 76.9 - - - +
440Q TRP* 1.3 75.9 + + - +
442Q GLY* 2.9 22.5 + - - -
444Q GLU* 3.8 16.1 - - + +
446Q ILE* 3.1 38.3 - - + +
447Q ARG* 3.9 4.4 - - - -
448Q GLN* 3.4 40.8 + - + +
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Residues in contact with TRP 440 (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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130Q ALA* 3.8 30.1 - - + -
133Q LEU* 3.7 39.0 - - + -
134Q MET* 3.9 26.0 - - + -
294Q ILE* 5.3 0.2 - - + -
298Q TYR* 3.5 39.0 - + + +
300Q TYR* 3.7 0.9 - - - +
301Q THR* 3.0 47.6 + - - +
302Q PHE* 3.6 19.2 - + - -
404Q LEU* 5.7 0.9 - - + -
407Q SER* 2.9 27.0 + - - -
408Q ILE* 4.4 5.0 - - + +
436Q LEU* 2.8 35.5 + - + +
439Q TYR* 1.3 90.1 - + - +
441Q GLN* 1.3 58.9 + - - +
442Q GLY 3.1 0.4 - - - -
448Q GLN* 4.7 0.2 - - - -
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Residues in contact with GLN 441 (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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297Q LYS* 3.9 29.6 - - - +
298Q TYR* 4.0 7.5 - - + -
300Q TYR* 3.5 19.9 - - - +
437Q ASP* 2.8 40.5 + - - +
438Q SER* 3.7 8.7 - - - +
439Q TYR 3.1 1.6 - - - -
440Q TRP* 1.3 76.8 - - - +
442Q GLY* 1.3 60.7 + - - +
443Q HIS* 3.4 37.0 + - + +
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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