Contacts of the strand formed by residues 152 - 158 (chain T) in PDB entry 2P8Z
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 LYS 152 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123T ASP 3.1 8.5 + - - +
124T GLY* 3.2 2.9 - - - -
125T ALA 2.8 30.9 + - - -
150T ARG 4.0 1.2 + - - -
151T ILE* 1.3 72.0 - - - +
153T PRO* 1.3 73.8 - - + +
154T VAL* 5.7 0.4 - - - -
197T LEU* 6.4 0.2 - - - -
199T ASP 6.1 0.4 - - - -
200T VAL* 4.0 19.3 - - + +
201T GLN 6.0 1.3 - - - -
208T THR* 5.4 6.8 - - - +
341T HIS* 2.9 44.6 + - - +
342T LEU* 3.5 5.8 - - + +
343T PRO* 3.8 22.7 - - + -
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Residues in contact with PRO 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125T ALA* 3.5 8.7 - - + +
127T VAL* 4.0 18.6 - - + -
143T LEU* 4.1 12.6 - - + -
147T LEU* 4.2 6.7 - - + -
151T ILE* 3.5 7.4 - - + +
152T LYS* 1.3 96.4 - - + +
154T VAL* 1.3 66.8 + - - +
155T VAL* 5.8 1.1 - - + -
185T VAL* 6.1 1.6 - - + -
189T VAL* 4.2 19.5 - - + -
200T VAL* 3.4 33.5 - - + +
202T VAL* 3.7 16.4 - - + +
208T THR* 5.2 1.2 - - - +
342T LEU* 4.6 0.2 - - - -
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Residues in contact with VAL 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125T ALA 3.0 8.8 + - - +
126T LEU* 3.5 11.3 - - + -
127T VAL* 2.6 32.9 + - - +
152T LYS* 5.7 0.7 - - - -
153T PRO* 1.3 77.8 - - - +
155T VAL* 1.3 56.7 + - - +
202T VAL* 4.5 1.6 - - - -
208T THR* 3.9 33.0 - - + +
337T MET* 3.3 43.1 - - + +
338T ILE* 5.3 1.8 - - + +
341T HIS* 4.1 12.6 - - + -
342T LEU* 4.0 20.0 - - + -
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Residues in contact with VAL 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T VAL* 3.3 19.7 - - + +
129T VAL* 4.2 11.0 - - + -
153T PRO* 5.7 0.7 - - + -
154T VAL* 1.3 76.7 - - - +
156T VAL* 1.3 78.9 + - - +
157T ILE* 4.0 16.8 - - + -
181T THR* 5.6 1.1 - - + -
182T VAL* 5.8 3.1 - - + -
185T VAL* 4.0 33.0 - - + -
202T VAL* 4.4 16.6 - - + -
208T THR 3.2 12.4 + - - +
209T VAL* 3.4 9.6 - - + -
210T ALA 2.9 22.3 + - - -
337T MET* 3.5 7.8 - - - +
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Residues in contact with VAL 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T LEU* 4.5 17.9 - - + -
126T LEU* 3.0 34.8 - - + -
127T VAL 2.9 6.5 + - - +
128T VAL* 3.6 6.7 - - - +
129T VAL 2.9 23.7 + - - -
155T VAL* 1.3 81.1 - - - +
157T ILE* 1.3 67.4 + - - +
158T ASN* 3.3 9.0 + - + +
210T ALA* 3.4 13.2 - - + +
211T PHE 5.0 0.7 - - - +
212T GLY* 5.1 4.5 - - - +
334T LEU* 3.3 28.3 - - + -
337T MET* 3.8 4.3 - - + -
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Residues in contact with ILE 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T VAL* 3.3 6.3 - - + +
130T ASP 4.5 1.8 - - - +
131T THR* 3.6 24.5 - - - +
155T VAL* 4.0 14.4 - - + -
156T VAL* 1.3 72.7 - - - +
158T ASN* 1.3 56.9 + - - +
160T VAL* 3.5 4.3 - - - +
178T PHE* 3.6 48.2 - - + +
181T THR* 4.2 17.5 - - + +
182T VAL* 4.1 11.9 - - + -
209T VAL* 4.3 1.1 - - + -
210T ALA 2.8 16.0 + - - +
211T PHE* 3.5 28.4 - - + -
212T GLY 3.0 24.9 + - - -
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Residues in contact with ASN 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T HIS 2.7 25.6 + - - +
31T GLY* 3.7 13.7 + - - -
35T LEU* 4.2 10.3 - - - +
128T VAL* 3.6 22.8 - - + +
129T VAL 2.7 11.2 + - - +
130T ASP* 4.7 0.9 - - - -
131T THR* 2.7 36.9 + - - -
156T VAL* 3.3 7.0 + - + +
157T ILE* 1.3 71.6 - - - +
159T LYS* 1.3 82.3 + - + +
160T VAL 3.2 3.8 - - - -
212T GLY 3.6 3.4 - - - +
213T SER* 3.8 1.9 + - - -
214T GLY* 2.9 25.8 + - - -
843T GNP 4.4 6.5 + - - -
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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