Contacts of the strand formed by residues 115 - 120 (chain B) in PDB entry 2POD
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 3.8 15.9 - - - +
114B THR* 1.3 73.9 - - - +
116B ARG* 1.3 72.7 + - - +
332B THR* 4.8 1.3 - - + -
335B SER* 3.6 44.0 - - - +
336B LEU* 4.0 9.6 - - + +
341B ALA* 3.8 17.3 - - + +
342B LEU 3.9 13.7 - - - +
343B VAL 3.9 16.4 - - - -
344B GLN* 3.9 5.4 - - + -
369B HIS* 3.6 4.5 - - - -
370B ILE* 2.7 58.5 + - + +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 1.3 75.0 - - - +
117B THR* 1.3 68.8 + - - +
171B THR* 3.0 42.0 + - - +
172B ALA* 3.5 15.0 - - - +
214B ASP* 2.9 28.2 + - - -
216B MSE 6.2 0.4 - - - +
241B PHE* 5.0 11.7 - - - -
342B LEU* 4.4 11.5 - - - +
343B VAL* 3.4 31.3 - - + +
344B GLN* 3.0 23.6 + - - +
368B GLY 3.5 11.7 - - - +
369B HIS* 3.3 24.6 + - + +
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE 3.4 1.2 + - - -
116B ARG* 1.3 86.8 + - - +
118B TYR* 1.3 62.9 + - - +
170B ILE* 4.1 24.7 - - + +
171B THR 4.9 2.1 + - - -
172B ALA* 4.7 3.6 + - - +
343B VAL* 4.6 1.1 - - - -
344B GLN 2.7 19.9 + - - -
346B SER* 2.8 29.3 + - - +
365B VAL* 4.1 12.6 - - + -
368B GLY 2.8 29.6 + - - +
369B HIS 4.1 2.2 - - - +
370B ILE* 3.9 18.7 - - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 1.3 78.6 + - - +
119B ASN* 1.3 61.9 + - - +
120B THR* 3.6 17.2 + - - -
170B ILE* 4.6 1.1 - - - -
172B ALA* 3.4 29.2 - - + +
174B LYS* 3.2 35.7 + - + -
216B MSE 4.0 15.9 - - + -
242B TRP* 3.6 19.6 - + - -
291B MSE 4.6 3.3 - - - -
318B ALA* 5.2 3.2 - - + +
319B PRO 5.2 0.6 + - - -
343B VAL* 3.6 35.0 - - + -
344B GLN 3.4 3.4 + - - -
345B GLU* 2.8 46.5 + - + +
346B SER* 3.1 26.1 + - - +
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TYR* 1.3 70.9 - - - +
120B THR* 1.3 76.6 + - - +
121B CYS* 3.3 12.4 + - - +
150B ASP* 3.5 22.8 + - - -
165B LEU* 3.8 27.3 - - + +
170B ILE* 4.1 10.0 - - + +
172B ALA 2.9 10.8 + - - +
173B MSE 3.3 4.3 - - - -
174B LYS 2.9 22.8 + - - -
346B SER* 3.3 7.3 + - - +
347B VAL* 5.3 0.4 - - - +
348B ARG* 2.9 39.4 + - - +
351B TYR* 4.5 3.3 + - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TYR* 3.6 11.2 + - - -
119B ASN* 1.3 72.8 + - - +
121B CYS* 1.3 51.0 + - - +
122B ALA 2.7 15.2 + - - +
174B LYS* 3.6 16.0 - - - -
176B TRP* 3.6 24.9 - - + -
322B CYS* 3.8 19.5 - - - -
345B GLU* 2.8 38.3 + - - +
346B SER 3.1 7.5 + - - -
347B VAL* 3.4 27.8 - - - +
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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