Contacts of the strand formed by residues 115 - 119 (chain C) in PDB entry 3Q29
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 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ALA 3.8 0.9 + - - -
114C LEU* 1.3 73.1 + - - +
116C LEU* 1.3 62.7 + - - +
117C ILE* 3.5 2.3 + - - +
227C ILE* 3.6 5.9 - - - +
228C ASN 3.1 32.3 + - - +
233C TRP* 5.7 1.6 - - - -
245C VAL* 3.5 26.8 - - - +
246C THR 3.6 1.8 - - - -
248C LEU* 3.8 7.2 - - - -
320C ALA 3.6 11.3 + - - -
321C THR* 3.8 14.6 + - - -
324C ASN* 3.0 22.8 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER* 1.3 72.4 - - - +
117C ILE* 1.3 63.3 + - - +
118C TYR* 5.0 0.7 - - + -
126C PRO* 4.1 17.3 - - + -
127C PRO 4.3 6.7 - - - +
133C ILE* 6.1 0.4 - - + -
148C LEU* 4.9 3.1 - - + -
225C MET* 3.9 32.8 - - + -
226C THR 3.9 12.3 - - - +
227C ILE* 4.4 11.0 - - + -
244C GLY 3.9 0.3 - - - +
245C VAL* 3.6 3.5 - - - -
246C THR* 2.9 50.5 + - + +
247C VAL 3.7 18.4 - - - +
248C LEU* 3.7 12.1 - - + +
249C PRO* 4.1 26.2 - - + -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER 4.0 8.7 - - - +
116C LEU* 1.3 76.7 - - - +
118C TYR* 1.3 64.5 + - - +
218C PHE* 3.8 19.0 - - + -
225C MET* 3.2 5.0 - - - +
226C THR* 2.9 43.9 + - + +
228C ASN* 4.0 31.9 - - + +
229C GLY 4.6 0.4 - - - +
232C ALA* 4.9 0.4 - - + -
233C TRP* 3.8 28.3 - - + +
236C ILE* 3.8 22.4 - - + -
243C TYR* 3.9 10.5 - - + -
244C GLY 3.5 10.3 - - - +
245C VAL* 4.5 11.0 - - + -
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Residues in contact with TYR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 5.0 1.6 - - + -
117C ILE* 1.3 78.0 - - - +
119C ASN* 1.3 61.8 + - - +
120C LYS* 3.5 27.0 + - + -
123C LEU* 3.2 31.0 - - + -
124C PRO 3.9 7.1 + - - -
126C PRO* 3.8 31.0 - - + +
218C PHE* 3.6 5.8 - - - -
224C ALA 3.2 10.8 - - - +
225C MET* 3.7 13.5 - - + -
243C TYR* 3.1 7.3 - - - -
244C GLY* 3.1 56.6 + - - -
246C THR* 3.8 31.9 - - + -
396C GOL 4.0 10.1 + - - -
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 1.3 70.6 - - - +
120C LYS* 1.3 53.5 + - - +
121C ASP* 3.1 22.9 + - - +
122C LEU* 3.2 34.8 + - + +
123C LEU* 2.7 38.2 + - - +
218C PHE* 3.6 13.9 + - + -
221C GLY* 4.1 17.0 - - - -
223C THR 4.3 1.6 + - - +
224C ALA* 2.7 16.2 + - - +
241C VAL* 3.7 22.3 - - - +
242C ASN 3.7 6.9 + - - +
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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