Contacts of the helix formed by residues 207 - 213 (chain I) in PDB entry 6PSS
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 THR 207 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206I ALA* 1.3 74.1 - - - +
208I ILE* 1.3 58.5 + - - +
209I ILE 3.3 1.1 - - - -
210I LEU* 3.1 24.5 + - + +
211I ARG* 2.9 32.9 + - - +
220I ILE* 4.0 7.0 - - + -
347I ILE* 3.9 7.9 - - + -
350I THR* 3.5 31.2 + - + -
351I LEU* 3.7 29.2 - - + +
354I ASP* 2.5 29.6 + - - +
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Residues in contact with ILE 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I VAL* 5.2 2.2 - - + -
204I LEU* 3.7 31.0 - - + -
205I PRO* 2.8 23.6 + - + +
207I THR* 1.3 77.2 - - - +
209I ILE* 1.3 57.2 + - - +
211I ARG* 3.2 6.9 + - - +
212I ALA* 2.9 29.1 + - - +
354I ASP* 3.4 19.0 + - - +
356I THR* 3.6 9.9 - - + +
362I ALA* 4.1 11.1 - - + +
365I GLU* 3.5 33.4 - - + +
366I ILE* 3.8 29.4 - - + -
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Residues in contact with ILE 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I LEU* 4.8 10.5 - - + -
186I PHE* 4.2 11.4 - - + -
196I VAL* 3.8 25.7 - - + +
198I ILE* 5.3 4.9 - - + -
206I ALA* 3.3 21.2 - - - +
208I ILE* 1.3 81.4 - - + +
210I LEU* 1.3 69.9 + - + +
212I ALA* 4.1 1.3 - - - -
213I LEU* 3.3 25.3 + - + +
366I ILE* 4.8 6.5 - - + -
385I PHE* 3.6 32.1 - - + -
389I PHE* 4.3 15.7 - - + -
425I ILE* 4.5 21.5 - - + -
429I MET* 4.4 0.9 - - - -
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Residues in contact with LEU 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206I ALA 3.6 8.5 - - - +
207I THR* 3.1 24.1 + - + +
209I ILE* 1.3 82.4 - - + +
211I ARG* 1.3 61.5 + - - +
213I LEU* 3.2 11.0 + - + -
214I ASN 3.3 0.5 + - - -
215I TYR* 2.9 34.2 + - + +
220I ILE* 3.7 26.5 - - + -
223I LEU* 6.3 0.4 - - + -
224I PHE* 3.7 25.1 - - + -
347I ILE* 4.2 0.7 - - + -
425I ILE* 5.1 3.1 - - + -
426I ILE* 3.7 29.8 - - + -
429I MET* 3.7 28.5 - - + -
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Residues in contact with ARG 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I THR* 2.9 22.1 + - - +
208I ILE* 3.7 5.4 - - - +
210I LEU* 1.3 74.4 - - - +
212I ALA* 1.3 60.0 + - - +
214I ASN* 2.9 19.1 + - - -
215I TYR 3.4 10.4 + - - +
216I THR* 3.4 13.7 - - - +
217I THR* 2.4 47.2 + - - +
220I ILE* 4.5 3.6 - - + -
351I LEU* 3.4 27.5 - - - +
354I ASP* 5.0 2.8 + - - -
356I THR* 3.5 22.4 + - - -
357I ASN* 3.4 42.1 + - - +
358I ASP* 4.1 5.9 + - - +
359I ARG* 3.4 15.3 + - - +
362I ALA* 4.0 12.3 - - + -
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Residues in contact with ALA 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I ILE 2.9 17.4 + - - +
209I ILE 4.2 2.2 - - - +
211I ARG* 1.3 76.2 - - - +
213I LEU* 1.3 55.8 + - - +
214I ASN 3.2 0.9 - - - -
359I ARG* 3.1 38.1 + - - -
362I ALA* 4.0 7.7 - - + +
363I LEU* 4.5 5.2 - - + -
366I ILE* 3.7 19.5 - - + -
385I PHE* 3.2 33.2 - - + -
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Residues in contact with LEU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I ILE* 3.3 21.0 + - + +
210I LEU* 3.2 9.5 + - - +
211I ARG 3.2 0.6 - - - -
212I ALA* 1.3 74.7 - - - +
214I ASN* 1.3 70.5 + - - +
215I TYR* 3.8 13.4 - - + -
359I ARG* 4.4 3.4 - - - +
385I PHE* 4.2 8.1 - - + -
390I PHE* 3.5 32.1 - - + -
422I LYS* 3.4 64.4 - - + +
425I ILE* 4.2 30.5 - - + -
426I ILE* 5.3 2.5 - - + -
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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