Contacts of the strand formed by residues 238 - 244 (chain J) 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 ILE 238 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J PRO* 5.6 1.9 - - - +
110J PRO* 3.8 22.4 - - + -
111J THR 4.1 4.0 - - - +
112J ALA* 3.7 29.2 - - + +
124J ILE* 4.6 4.5 - - + -
139J LEU* 4.8 0.2 - - + -
182J ALA* 3.9 7.9 - - + +
185J ILE* 4.1 20.6 - - + -
186J GLN* 3.7 44.9 + - + +
189J LEU* 3.7 23.1 - - + -
235J GLU 3.3 16.0 + - - +
236J TRP* 3.3 4.2 - - - +
237J MET* 1.3 77.2 - - - +
239J LEU* 1.3 63.6 + - - +
240J THR* 3.7 3.6 + - - +
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Residues in contact with LEU 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334I GLY* 4.8 9.9 - - - +
25J ALA 5.5 2.0 - - - +
27J PRO* 6.2 2.9 - - + -
30J ILE* 3.8 18.2 - - + -
107J LEU* 4.5 7.7 - - + +
110J PRO* 3.3 2.8 - - - +
111J THR* 2.7 48.7 + - + +
112J ALA 5.2 0.2 - - - -
113J HIS* 4.1 32.1 - - + +
236J TRP 5.0 7.6 - - - +
237J MET 3.5 3.3 + - - +
238J ILE* 1.3 74.1 - - - +
240J THR* 1.3 61.8 + - + +
241J VAL* 3.3 24.5 - - + +
242J LEU* 4.2 24.5 - - + -
243J PRO* 5.2 2.7 - - + -
303J VAL* 5.0 4.3 - - + -
307J LEU* 4.6 10.3 - - + -
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Residues in contact with THR 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PRO* 4.0 30.5 - - + -
31J ARG* 5.1 7.4 + - - +
106J GLU* 3.9 1.6 - - - +
107J LEU* 2.9 38.3 + - - +
110J PRO* 4.4 16.1 - - - +
186J GLN* 4.1 22.0 - - - +
238J ILE 4.4 2.0 - - - +
239J LEU* 1.3 76.4 - - - +
241J VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PRO* 3.5 43.7 - - + +
30J ILE* 3.3 17.1 - - + +
31J ARG* 4.0 13.0 - - + +
104J HIS* 3.5 41.3 - - + -
105J ILE 3.2 8.3 - - - +
106J GLU* 4.0 9.0 - - + -
107J LEU* 5.0 0.9 - - - -
239J LEU* 3.3 20.3 - - + +
240J THR* 1.3 83.5 - - + +
242J LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE* 4.2 1.1 - - - -
104J HIS* 3.3 2.3 - - - -
105J ILE* 2.6 63.8 + - + +
107J LEU* 4.3 11.0 - - + -
239J LEU* 4.2 20.6 - - + -
241J VAL* 1.3 73.7 - - - +
243J PRO* 1.3 73.1 - - + +
244J VAL 3.6 0.5 + - - -
269J TYR* 4.1 6.5 - - + -
272J VAL* 3.8 28.9 - - + -
303J VAL* 4.3 22.4 - - + -
306J LEU* 3.8 22.4 - - + -
307J LEU* 4.7 8.7 - - + -
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Residues in contact with PRO 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331I ARG 3.6 25.4 - - - +
1332I SER* 3.6 14.9 + - - +
1333I LEU 4.0 12.6 - - - +
1334I GLY 5.1 0.9 - - - +
30J ILE* 3.7 32.1 - - + +
33J TRP* 4.7 4.5 - - + -
102J MET* 3.8 12.3 - - + -
103J GLY 3.6 7.9 - - - +
239J LEU* 5.2 3.1 - - + -
241J VAL 3.9 5.4 - - - +
242J LEU* 1.3 93.5 - - + +
244J VAL* 1.3 60.4 + - - +
269J TYR* 2.8 19.6 + - - -
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Residues in contact with VAL 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332I SER* 3.7 2.5 - - - -
38J VAL* 3.8 20.0 - - + -
56J LEU* 5.3 3.1 - - + -
62J PHE* 3.9 12.3 - - + -
102J MET* 3.3 23.7 - - - +
103J GLY* 3.0 32.1 + - - +
105J ILE* 3.7 31.4 - - + -
242J LEU 4.3 0.4 - - - +
243J PRO* 1.3 73.2 - - - +
245J LEU* 1.3 65.1 + - - +
250J ARG* 4.2 5.8 - - - +
269J TYR* 3.5 26.5 - - + -
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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