Contacts of the strand formed by residues 172 - 178 (chain J) in PDB entry 3CII
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 172 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D SER* 5.4 1.6 + - - -
154D GLU* 5.4 5.0 - - - +
155D HIS* 2.9 28.8 + - - -
170J SER* 4.2 5.2 - - - +
171J PRO* 1.3 79.4 - - - +
173J SER* 1.3 65.5 + - - +
210J VAL* 6.2 0.2 - - - -
211J LEU 3.3 6.7 - - - -
212J GLN* 4.3 13.0 - - - -
225J ILE* 4.3 15.9 - - - +
226J ILE* 3.6 26.9 - - - +
228J HIS* 4.2 3.6 + - - -
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Residues in contact with SER 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J LEU* 3.8 10.9 - - - +
172J SER* 1.3 76.5 - - - +
174J TRP* 1.3 74.9 + - - +
210J VAL* 3.4 6.8 - - - +
211J LEU* 2.8 45.9 + - - +
225J ILE* 4.5 2.3 - - - +
226J ILE 3.0 9.8 + - - -
228J HIS* 3.3 42.4 + - - -
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Residues in contact with TRP 174 (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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138J ARG 3.3 18.8 + - - -
140J TRP* 3.3 42.1 - + + +
143J SER* 3.3 22.0 - - - -
154J LEU* 4.3 17.8 - - + +
155J LEU* 3.9 9.9 - - - +
173J SER* 1.3 85.9 + - - +
175J ILE* 1.3 61.1 + - - +
208J CYS* 3.6 20.0 - - + -
209J ALA 3.3 8.1 - - - -
210J VAL* 3.3 26.7 - - + +
219J ALA* 4.0 13.7 - - + -
220J GLN 3.3 23.6 - - - -
221J CYS* 3.9 7.4 - - - -
223J SER 3.2 21.8 - - - -
225J ILE* 3.4 23.3 - - + +
226J ILE 3.2 15.7 + - - +
227J TYR* 4.9 1.3 - - - -
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Residues in contact with ILE 175 (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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140J TRP* 3.3 14.2 + - - -
154J LEU* 3.8 4.7 - - - -
155J LEU* 3.3 18.6 - - + +
156J SER* 5.3 1.1 - - - -
157J ILE* 4.2 19.5 - - + +
173J SER 3.5 8.3 + - - +
174J TRP* 1.3 79.1 - - - +
176J GLY* 1.3 53.7 + - - +
177J VAL* 2.5 47.8 + - + +
194J PHE* 4.6 1.8 - - + -
209J ALA* 3.4 29.2 + - + +
210J VAL 4.4 0.2 - - - +
211J LEU* 4.2 16.6 - - + -
216J LEU* 3.4 33.4 - - + -
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Residues in contact with GLY 176 (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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140J TRP* 4.4 0.9 - - - -
154J LEU* 3.6 17.6 - - - +
155J LEU 2.9 15.5 + - - -
156J SER* 4.9 7.0 - - - +
175J ILE* 1.3 66.4 - - - +
177J VAL* 1.3 65.9 + - - +
188J THR* 3.4 20.4 - - - +
189J MET* 3.5 34.1 + - - +
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Residues in contact with VAL 177 (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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140J TRP* 4.6 1.8 + - - -
156J SER* 6.4 1.1 - - - -
157J ILE 6.3 0.7 - - - +
175J ILE* 2.5 29.2 + - + +
176J GLY* 1.3 80.4 - - - +
178J PHE* 1.3 64.5 + - - +
186J TRP* 3.5 24.2 - - + -
187J VAL 3.3 9.0 - - - +
188J THR* 4.5 2.5 - - + -
194J PHE* 3.7 57.0 - - + -
198J ILE* 4.9 1.6 - - + -
208J CYS* 3.9 1.0 - - - +
209J ALA* 3.1 31.5 + - + +
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Residues in contact with PHE 178 (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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140J TRP* 3.7 29.2 - + + -
177J VAL* 1.3 74.3 - - - +
179J ARG* 1.3 78.6 + - - +
180J ASN* 3.5 23.6 - - - -
186J TRP* 3.9 7.4 - - - -
187J VAL* 2.9 45.1 + - + +
188J THR 4.2 11.9 - - - -
189J MET* 3.9 25.6 - - + -
207J ASN 3.2 12.6 - - - +
208J CYS* 4.4 11.2 - - - -
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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