Contacts of the helix formed by residues 311 - 316 (chain X) in PDB entry 4HSC
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 ASN 311 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110X ASN* 3.8 20.8 + - - +
114X TYR* 2.9 20.0 + - - +
309X PRO* 3.4 10.1 - - - +
310X ASN* 1.3 99.4 + - - +
312X PRO* 1.3 76.2 - - + +
313X ALA 4.3 0.2 - - - +
314X ASP* 2.9 34.0 + - - +
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Residues in contact with PRO 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X ILE* 4.7 0.4 - - - -
110X ASN* 3.5 9.6 - - - +
113X ILE* 3.6 38.1 - - + -
114X TYR* 3.3 35.7 - - + +
310X ASN 4.8 0.4 - - - +
311X ASN* 1.3 85.3 - - + +
313X ALA* 1.3 59.7 + - - +
314X ASP 3.3 0.9 + - - -
315X VAL* 3.4 22.2 + - - +
316X PHE* 3.6 7.2 - - - -
438X LEU* 3.6 34.6 - - + +
439X LYS 3.9 4.7 - - - +
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Residues in contact with ALA 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106X THR* 3.7 31.7 + - + +
109X ILE* 4.0 18.8 - - + -
110X ASN* 2.7 36.2 + - - +
198X ASN* 4.4 0.7 + - - -
311X ASN 3.1 0.6 + - - -
312X PRO* 1.3 73.2 - - - +
314X ASP* 1.3 65.4 + - - +
315X VAL 3.0 2.6 + - - -
316X PHE* 3.1 23.2 + - - +
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Residues in contact with ASP 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X THR* 5.7 2.6 - - - +
110X ASN* 5.6 0.2 + - - -
198X ASN* 3.0 31.1 + - - +
199X PRO 5.1 1.7 - - - +
309X PRO* 4.1 10.5 - - + -
310X ASN* 3.1 17.7 + - - +
311X ASN* 2.9 44.1 + - - +
313X ALA* 1.3 80.0 - - - +
315X VAL* 1.3 55.7 + - - +
316X PHE 3.4 0.2 - - - -
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Residues in contact with VAL 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178X LEU* 4.1 11.7 - - + -
197X ARG* 3.0 35.0 + - - +
198X ASN* 3.0 18.1 + - - +
199X PRO 6.1 0.2 - - - -
200X GLN* 4.9 4.9 - - - +
309X PRO* 3.4 35.4 - - + -
312X PRO 3.4 15.9 - - - +
314X ASP* 1.3 77.6 - - - +
316X PHE* 1.3 84.0 + - + +
338X PHE* 4.0 18.6 - - + -
438X LEU* 4.2 7.0 - - + -
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Residues in contact with PHE 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X THR* 5.8 0.2 + - - -
109X ILE* 3.7 31.2 - - + -
113X ILE* 4.1 1.1 - - + -
178X LEU* 3.5 29.6 - - + -
193X VAL* 4.8 1.8 - - + -
195X THR* 3.4 21.1 - - + -
196X LYS 3.8 2.2 - - - -
198X ASN* 3.2 18.3 + - - -
312X PRO 3.6 14.4 - - - -
313X ALA* 3.1 12.1 + - - +
315X VAL* 1.3 92.0 - - + +
317X ASP* 1.3 72.2 + - - +
318X LYS* 3.5 1.9 + - - -
320X VAL* 4.0 17.9 - - + -
325X LEU* 3.6 34.1 - - + -
336X PRO* 5.7 2.7 - - + -
438X LEU* 3.8 14.6 - - + -
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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