Contacts of the helix formed by residues 192 - 200 (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 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D PHE* 3.3 24.2 - - - +
155D ILE* 5.8 0.4 - - - -
185D PHE* 6.3 0.2 - - - -
186D TRP* 3.4 38.0 + - - +
189D ARG* 2.7 21.9 + - - -
190D PRO* 4.2 1.0 - - - +
191D GLU* 1.3 77.5 - - - +
193D LEU* 1.3 66.7 + - - +
194D HIS 3.1 3.6 + - - -
195D GLN* 3.3 4.1 + - - +
196D VAL* 2.8 31.2 + - - +
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Residues in contact with LEU 193 (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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190D PRO* 3.0 29.9 + - + +
191D GLU 3.2 0.6 - - - -
192D SER* 1.3 79.3 + - - +
194D HIS* 1.3 61.5 + - - +
196D VAL* 3.8 4.4 - - - +
197D SER* 2.7 31.6 + - - -
439D ASN* 3.7 12.6 - - + +
440D VAL* 3.8 24.9 - - + -
443D VAL* 4.1 8.3 - - + -
481D ASN* 3.7 43.5 - - + +
482D PHE* 3.8 30.3 - - + -
484D GLU* 5.1 2.7 - - + +
485D VAL* 3.9 7.6 - - + -
489D TYR* 5.2 0.7 - - + -
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Residues in contact with HIS 194 (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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152D ILE* 3.2 23.4 - - + +
191D GLU 4.3 6.8 + - - +
192D SER 3.1 1.2 + - - -
193D LEU* 1.3 79.1 - - - +
195D GLN* 1.3 64.5 + - - +
197D SER* 3.1 14.0 + - - -
198D PHE* 3.1 12.5 + - + +
300D THR* 3.0 26.0 + - - +
302D VAL* 4.1 15.9 - - + +
439D ASN 4.8 0.6 + - - +
442D GLN* 3.4 43.3 + - + +
443D VAL* 3.7 27.4 - - + +
446D PHE* 4.5 17.9 - + + +
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Residues in contact with GLN 195 (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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129D PRO* 4.1 12.1 - - - +
150D THR* 3.0 31.1 + - - +
152D ILE* 3.4 11.6 - - + +
153D PHE* 3.3 45.0 + - + +
154D PHE* 3.5 37.2 - - + +
192D SER 3.3 2.4 + - - +
194D HIS* 1.3 75.5 - - - +
196D VAL* 1.3 56.2 + - - +
198D PHE* 3.0 15.6 + - - +
199D LEU* 2.7 45.2 + - - +
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Residues in contact with VAL 196 (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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154D PHE* 3.9 8.7 - - + -
183D TRP* 4.2 14.8 - - + -
186D TRP* 3.7 31.6 - - + -
192D SER* 2.8 39.2 + - - +
193D LEU* 3.8 5.4 - - + +
195D GLN* 1.3 75.7 - - - +
197D SER* 1.3 58.4 + - - +
199D LEU* 3.4 3.0 + - - +
200D PHE* 3.0 50.0 + - + +
463D ILE* 5.0 1.5 - - + +
482D PHE* 4.2 19.3 - - + -
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Residues in contact with SER 197 (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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193D LEU* 2.7 21.5 + - - +
194D HIS 3.1 5.6 + - - -
196D VAL* 1.3 75.6 - - - +
198D PHE* 1.3 63.5 + - - +
201D SER* 3.5 18.5 + - - -
443D VAL* 3.6 16.8 - - - +
446D PHE* 3.8 21.8 - - - -
447D TYR* 6.4 1.1 - - - -
459D LEU* 3.6 14.5 - - - +
463D ILE* 5.6 0.2 - - - -
482D PHE* 4.9 1.6 - - - -
489D TYR* 2.8 31.1 + - - -
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Residues in contact with PHE 198 (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* 3.5 30.5 - - - -
150D THR* 4.0 10.5 - - + -
151D PRO* 4.5 15.5 - - + -
152D ILE* 4.8 5.8 - - + -
194D HIS* 3.1 11.6 + - + +
195D GLN* 3.0 27.0 + - - +
197D SER* 1.3 75.5 - - - +
199D LEU* 1.3 68.6 + - - +
201D SER* 2.8 25.6 + - - +
203D ARG* 3.5 53.8 - - + -
204D GLY* 4.1 2.5 + - - -
215D TYR* 5.6 1.6 - + - -
446D PHE* 4.2 26.2 - + + -
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Residues in contact with LEU 199 (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* 3.0 25.3 + - + +
128D ASP* 3.7 42.6 - - - +
129D PRO* 3.9 11.7 - - + -
154D PHE* 3.8 19.5 - - + -
168D GLN* 5.8 2.2 - - - +
186D TRP* 3.9 22.4 - - + -
195D GLN* 2.7 28.9 + - - +
196D VAL* 3.6 4.9 - - - +
198D PHE* 1.3 78.9 - - - +
200D PHE* 1.3 67.0 + - + +
201D SER 3.3 0.2 - - - -
204D GLY* 3.2 17.1 - - - -
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Residues in contact with PHE 200 (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* 3.4 26.2 - - - +
183D TRP* 3.7 23.3 - + - -
186D TRP* 3.8 30.1 - + - -
196D VAL* 3.0 34.4 + - + +
198D PHE 3.3 0.4 - - - -
199D LEU* 1.3 83.4 - - + +
201D SER* 1.3 59.8 + - - +
459D LEU* 3.4 28.7 - - + +
462D ASN* 3.1 56.7 - - + +
463D ILE* 3.6 13.2 - - + -
466D HIS* 4.0 22.0 - + + -
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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