Contacts of the helix formed by residues 297 - 304 (chain A) in PDB entry 5F85
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 PHE 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.4 25.1 - + - -
183A ALA* 3.5 23.1 - - + -
184A TRP* 3.7 29.2 - + - -
185A THR* 3.5 34.3 - - + +
191A PRO* 3.6 20.4 - - + -
200A ILE* 5.6 2.2 - - + -
296A SER* 1.3 70.8 - - - +
298A ARG* 1.3 61.4 + - - +
299A LEU 3.3 0.8 + - - -
300A LYS* 3.1 21.5 + - - +
301A HIS* 2.8 25.4 + - + -
318A GLU* 3.9 12.8 - - - -
501A UDP 3.7 11.0 - - - +
502A GOL 2.9 37.4 + - - +
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Residues in contact with ARG 298 (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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228A PHE* 3.5 17.6 - - - -
229A ARG 3.0 26.5 + - - -
230A GLY* 3.2 5.3 - - - -
237A ARG* 3.7 8.7 - - - +
278A PHE* 4.7 2.0 - - + -
281A HIS* 4.7 9.1 + - - +
288A PHE 3.8 22.7 - - - -
289A ASN* 3.5 9.6 + - - +
290A PHE 5.0 0.8 + - - +
296A SER* 3.1 7.5 + - - +
297A PHE* 1.3 78.8 - - - +
299A LEU* 1.3 66.0 + - - +
301A HIS* 2.9 24.6 + - - +
302A LEU* 3.5 21.9 + - + -
501A UDP 2.8 85.9 + - - +
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Residues in contact with LEU 299 (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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289A ASN* 3.2 35.6 + - + +
296A SER 3.5 9.8 + - - +
297A PHE 3.3 1.4 - - - -
298A ARG* 1.3 76.5 - - - +
300A LYS* 1.3 63.9 + - - +
302A LEU* 3.0 22.7 + - - +
303A PHE* 3.4 31.7 - - + -
309A VAL* 3.8 19.1 - - + -
311A HIS* 3.8 17.9 - - + +
318A GLU* 5.4 0.4 - - - +
320A PHE* 4.8 1.3 - - + -
321A TYR* 3.6 39.3 - - + +
324A LEU* 4.1 18.8 - - + -
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Residues in contact with LYS 300 (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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185A THR* 4.1 10.8 + - - +
186A PHE* 3.6 36.2 - - + +
203A TRP* 3.5 46.2 - - + -
296A SER 5.2 0.2 + - - -
297A PHE* 3.1 45.6 + - - +
299A LEU* 1.3 79.8 - - - +
301A HIS* 1.3 72.0 + - - +
302A LEU 3.5 0.2 + - - -
303A PHE* 3.7 21.8 + - - +
304A LEU 4.0 2.9 + - - -
318A GLU* 5.1 4.0 + - - +
320A PHE* 3.9 16.2 - - + -
367A ILE* 4.0 6.6 - - + +
371A LEU* 3.8 17.9 - - + -
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Residues in contact with HIS 301 (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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200A ILE* 4.2 15.3 - - + +
201A GLY 5.8 0.6 + - - -
203A TRP* 3.7 9.3 - + - -
206A MET* 3.4 35.1 - - + +
210A LEU* 3.6 19.4 - - + +
278A PHE* 3.3 55.4 - + + -
297A PHE* 2.8 28.7 + - + -
298A ARG 2.9 8.0 + - - +
300A LYS* 1.3 95.5 - - - +
302A LEU* 1.3 67.2 + - + +
303A PHE 3.3 0.2 - - - -
304A LEU 3.3 9.2 + - - -
305A CYS* 3.8 9.2 + - - -
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Residues in contact with LEU 302 (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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278A PHE* 5.9 1.1 - - + -
281A HIS* 3.8 31.0 - - + -
287A LEU* 3.7 28.6 - - + +
288A PHE 3.7 16.6 - - - +
289A ASN* 3.7 30.3 - - + -
298A ARG* 3.6 28.5 - - + +
299A LEU* 3.0 9.7 + - - +
301A HIS* 1.3 81.4 - - + +
303A PHE* 1.3 62.0 + - - +
305A CYS* 3.2 21.4 + - - +
306A LYS 4.3 0.9 + - - -
307A SER 4.3 2.9 + - - -
309A VAL* 3.7 23.6 - - + +
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Residues in contact with PHE 303 (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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299A LEU* 3.4 48.0 - - + -
300A LYS* 3.9 4.0 - - - +
301A HIS 3.3 0.4 - - - -
302A LEU* 1.3 77.4 - - - +
304A LEU* 1.3 59.2 + - - +
305A CYS 3.1 0.7 - - - -
306A LYS* 3.2 16.6 + - - -
307A SER 5.0 3.3 - - - +
309A VAL* 3.8 26.0 - - + -
324A LEU* 3.8 27.8 - - + -
329A HIS 3.2 24.0 - - - -
330A TYR* 4.0 15.9 - + + -
360A ALA* 4.8 1.7 - - - +
363A GLY* 3.6 26.5 - - - +
364A TYR* 3.3 19.2 + - - +
367A ILE* 3.6 30.7 - - + -
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Residues in contact with LEU 304 (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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203A TRP* 3.6 25.6 - - + -
207A ARG* 3.8 36.6 - - + +
210A LEU* 3.2 45.3 - - + +
211A GLU 5.1 0.2 - - - +
214A ALA* 3.4 8.1 - - - +
300A LYS 4.1 3.4 - - - +
301A HIS 3.3 3.3 + - - +
302A LEU 3.2 1.4 - - - -
303A PHE* 1.3 74.9 - - - +
305A CYS* 1.3 57.7 + - - +
306A LYS 3.3 0.7 - - - -
364A TYR* 3.6 36.0 - - + +
367A ILE* 3.7 24.9 - - + -
368A TRP* 3.9 16.4 - - + +
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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