Contacts of the strand formed by residues 233 - 240 (chain J) in PDB entry 5HHM
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 GLN 233 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122J PRO* 3.6 25.7 - - - +
212J VAL 3.7 1.0 - - - +
213J GLN* 3.3 9.9 + - - +
214J PHE* 2.9 39.3 + - + +
229J LYS 4.7 1.7 - - - +
230J PRO* 4.5 1.6 - - - +
231J VAL* 3.0 30.7 + - + +
232J THR* 1.4 74.3 - - - +
234J ILE* 1.3 64.5 + - - +
235J VAL* 3.4 26.3 - - + +
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Residues in contact with ILE 234 (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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209J ARG* 4.8 0.9 - - - +
211J GLN* 3.7 33.2 - - + +
212J VAL 3.7 2.7 - - - +
213J GLN* 3.3 30.5 - - + +
233J GLN* 1.3 77.0 + - - +
235J VAL* 1.3 61.0 + - - +
236J SER* 3.4 23.7 + - - +
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Residues in contact with VAL 235 (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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122J PRO* 4.6 1.6 - - + -
123J PRO* 3.4 40.4 - - + +
124J GLU* 4.7 1.1 - - - -
125J VAL* 3.4 30.9 - - + +
212J VAL 3.0 30.1 + - - +
233J GLN* 3.4 33.9 - - + +
234J ILE* 1.3 72.6 - - - +
236J SER* 1.3 65.8 + - - +
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Residues in contact with SER 236 (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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125J VAL* 4.3 7.2 - - - +
209J ARG* 2.9 37.9 + - - -
210J CYS 3.3 9.6 - - - -
211J GLN* 3.9 2.6 - - - -
234J ILE* 3.4 19.1 + - - +
235J VAL* 1.3 77.1 + - - +
237J ALA* 1.3 61.9 + - - +
238J GLU* 6.0 0.7 - - - -
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Residues in contact with ALA 237 (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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125J VAL* 3.6 36.6 - - + +
126J ALA* 3.8 10.5 - - - +
127J VAL* 3.8 14.7 - - + +
209J ARG* 3.4 3.7 - - - +
210J CYS* 2.8 32.4 + - - +
236J SER* 1.3 75.7 - - - +
238J GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 238 (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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126I SER* 3.9 9.0 + - - -
127I LYS* 3.5 30.5 + - - +
127J VAL* 4.4 5.5 - - - +
207J HIS* 2.7 40.0 + - + +
208J PHE 3.4 7.6 - - - +
209J ARG* 4.2 15.2 - - + -
236J SER* 6.0 0.3 - - - -
237J ALA* 1.3 76.1 - - - +
239J ALA* 1.3 62.5 + - - +
240J TRP* 4.2 11.1 + - + -
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Residues in contact with ALA 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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126I SER* 3.9 16.6 - - - +
127I LYS* 5.2 1.8 - - - +
127J VAL* 4.0 17.0 - - + -
129J GLU* 4.2 12.8 - - + +
143J LEU* 4.8 0.4 - - + -
201J TRP* 4.7 6.7 - - + -
207J HIS* 3.1 23.7 - - - -
208J PHE* 3.0 24.3 + - + +
238J GLU* 1.3 76.5 - - - +
240J TRP* 1.3 66.5 + - - +
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Residues in contact with TRP 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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129J GLU* 3.9 8.1 + - - +
201J TRP* 3.6 20.3 - - - -
204J PRO* 3.3 27.6 - - + +
205J ARG* 3.7 15.5 - - - -
206J ASN 3.4 14.1 - - - -
207J HIS* 3.6 39.7 - + + -
208J PHE* 4.7 0.2 - - - -
238J GLU* 4.2 10.3 + - + -
239J ALA* 1.3 77.7 - - - +
241J GLY* 1.3 67.1 + - - +
242J ARG* 4.0 11.4 + - - +
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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