Contacts of the helix formed by residues 201 - 205 (chain D) in PDB entry 1F4J
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 SER 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ARG* 3.3 8.0 + - - -
197D SER 3.5 11.8 + - - -
198D PHE* 2.8 21.7 + - - -
200D PHE* 1.3 82.2 - - - +
202D ASP* 1.3 67.4 + - - +
203D ARG* 3.2 18.7 + - - +
204D GLY 2.8 12.0 + - - -
446D PHE* 4.5 13.3 - - - -
451D LEU* 4.6 15.0 - - - -
455D GLN* 5.9 2.0 - - - -
458D ARG 6.2 0.2 - - - -
459D LEU* 4.4 8.5 - - - +
462D ASN* 4.8 2.2 - - - -
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Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ARG* 5.2 1.2 + - - +
201D SER* 1.3 73.9 + - - +
203D ARG* 1.3 55.3 + - + +
204D GLY 2.8 11.3 + - - -
205D ILE* 3.1 11.6 + - - +
244D ASN* 3.5 33.4 - - + +
245D LEU 4.8 5.0 - - - +
451D LEU* 5.7 0.7 - - - +
455D GLN* 3.7 20.4 + - - +
458D ARG* 2.9 49.7 + - - +
462D ASN* 5.2 1.5 + - - +
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Residues in contact with ARG 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ASN* 3.9 14.8 + - - +
198D PHE* 3.5 48.6 - - + -
201D SER* 3.0 12.7 + - - +
202D ASP* 1.3 75.8 - - + +
204D GLY* 1.3 61.9 + - - +
205D ILE* 3.2 2.3 + - - -
206D PRO* 3.5 12.9 - - - +
213D ASN* 3.8 21.2 - - - +
215D TYR* 4.8 5.5 + - - -
242D ILE* 3.6 43.8 - - - +
244D ASN* 3.9 13.6 - - - +
446D PHE* 6.3 0.7 - - + -
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Residues in contact with GLY 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL 3.8 1.2 - - - +
127D ARG* 3.5 5.7 - - - -
128D ASP 3.4 27.4 + - - +
198D PHE* 4.1 1.2 + - - -
199D LEU* 3.2 31.6 + - - -
201D SER 2.8 9.4 + - - -
202D ASP 2.8 3.8 + - - -
203D ARG* 1.3 79.1 - - - +
205D ILE* 1.3 66.1 + - - +
206D PRO* 3.6 2.5 - - - +
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 4.1 14.8 - - - -
126D VAL* 3.8 1.8 - - - -
127D ARG* 3.6 46.4 - - + +
130D ARG* 4.1 7.0 - - - +
202D ASP 3.1 8.3 + - - +
204D GLY* 1.3 85.4 - - - +
206D PRO* 1.3 63.8 - - - +
244D ASN* 3.5 1.9 - - - +
245D LEU* 2.9 43.6 + - + +
247D VAL* 4.7 10.5 - - + -
250D ALA* 3.7 35.0 - - + -
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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