Contacts of the helix formed by residues 192 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A PHE* 3.1 25.3 + - - -
155A ILE* 5.5 1.1 - - - -
185A PHE* 6.0 0.2 - - - -
186A TRP* 3.3 41.9 + - - +
189A ARG* 2.8 21.9 + - - -
190A PRO* 2.7 2.1 - - - +
191A GLU* 1.3 79.0 - - - +
193A LEU* 1.3 66.3 + - - +
194A HIS 3.2 0.6 + - - -
195A GLN* 3.5 3.8 + - - -
196A VAL* 3.0 28.9 + - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 2.8 31.2 + - + +
191A GLU 3.2 0.4 - - - -
192A SER* 1.3 77.2 + - - +
194A HIS* 1.3 64.7 + - - +
196A VAL* 3.2 6.6 + - + +
197A SER* 2.8 27.0 + - - -
439A ASN* 3.4 22.0 - - + +
440A VAL* 4.1 7.4 - - + -
443A VAL* 4.1 10.5 - - + -
481A ASN* 4.0 30.3 - - + +
482A PHE* 3.9 34.0 - - + -
484A GLU* 5.5 0.2 - - + -
485A VAL* 3.7 22.4 - - + -
489A TYR* 5.6 0.4 - - + -
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 3.4 24.7 - - + +
191A GLU 4.3 7.0 + - - +
192A SER 3.2 0.6 + - - -
193A LEU* 1.3 77.3 - - - +
195A GLN* 1.3 63.3 + - - +
197A SER* 3.0 14.6 + - - -
198A PHE* 3.1 12.2 + - + +
300A THR* 2.8 27.6 + - - +
302A VAL* 4.5 9.0 - - + +
439A ASN 4.8 0.2 + - - -
442A GLN* 3.3 51.6 + - + +
443A VAL* 3.5 25.5 - - + +
446A PHE* 4.3 19.2 - + + +
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PRO* 4.3 9.3 - - - +
150A THR* 2.7 34.7 + - - +
152A ILE* 3.3 18.0 - - + +
153A PHE* 3.3 33.6 + - - +
154A PHE* 3.5 35.9 - - + +
192A SER 3.5 2.4 + - - -
194A HIS* 1.3 78.5 - - - +
196A VAL* 1.3 56.3 + - - +
198A PHE* 3.7 12.0 - - - +
199A LEU* 2.8 43.7 + - - +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A PHE* 3.6 24.7 - - + -
183A TRP* 4.4 15.0 - - + -
186A TRP* 3.9 20.0 - - + -
192A SER* 3.0 34.1 + - - +
193A LEU* 3.5 7.0 - - + +
195A GLN* 1.3 77.3 - - - +
197A SER* 1.3 65.2 + - - +
199A LEU* 4.3 2.0 - - - -
200A PHE* 3.1 45.8 + - + +
459A LEU* 4.8 0.2 - - - +
463A ILE* 4.9 1.8 - - + -
482A PHE* 4.4 17.9 - - + -
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Residues in contact with SER 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 2.8 15.4 + - - -
194A HIS 3.0 9.2 + - - -
196A VAL* 1.3 76.8 - - - +
198A PHE* 1.3 62.6 + - - +
201A SER* 3.4 22.0 + - - -
443A VAL* 3.6 10.5 - - - +
446A PHE* 3.8 25.5 - - - -
447A TYR* 5.7 0.8 - - - +
459A LEU* 3.7 13.1 - - - +
482A PHE* 4.9 1.0 - - - -
489A TYR* 2.9 37.9 + - - -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN* 3.7 31.0 - - - -
150A THR* 3.8 22.9 - - - -
151A PRO* 4.8 10.3 - - + -
152A ILE* 4.8 6.1 - - + -
194A HIS* 3.1 12.6 + - + +
195A GLN* 3.7 19.5 - - - +
196A VAL 3.2 0.2 - - - -
197A SER* 1.3 78.9 - - - +
199A LEU* 1.3 65.1 + - - +
201A SER* 2.8 22.7 + - - +
203A ARG* 3.6 53.4 - - + -
204A GLY* 4.2 2.8 + - - -
215A TYR* 5.4 3.1 - + - -
446A PHE* 4.1 27.5 - + + -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.1 24.9 + - + -
128A ASP* 3.5 46.7 - - - +
129A PRO* 3.7 11.7 - - + -
154A PHE* 3.7 20.6 - - + -
186A TRP* 4.0 11.7 - - + -
195A GLN* 2.8 30.0 + - - +
196A VAL* 3.4 3.3 + - - +
198A PHE* 1.3 77.5 - - - +
200A PHE* 1.3 78.0 + - + +
201A SER 3.2 0.2 - - - -
204A GLY* 3.2 18.3 - - - -
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.5 27.8 - - - +
183A TRP* 3.8 19.3 - + - -
186A TRP* 3.6 31.4 - + - -
196A VAL* 3.1 34.9 + - + +
198A PHE 3.3 0.2 - - - -
199A LEU* 1.3 84.3 - - + +
201A SER* 1.3 60.2 + - - +
459A LEU* 3.6 13.8 - - + +
462A ASN* 3.1 52.5 + - + +
463A ILE* 3.5 29.4 - - + -
466A HIS* 4.0 23.3 - + + -
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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