Contacts of the strand formed by residues 247 - 252 (chain C) in PDB entry 2IGT
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 GLY 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TRP* 3.9 17.3 - - - -
206C ASP 3.5 4.0 + - - +
207C ILE* 3.4 6.0 - - - +
208C ILE 3.1 23.2 + - - -
241C LEU* 4.0 6.3 - - - +
245C ALA* 3.7 2.0 - - - +
246C LEU* 1.3 81.8 - - - +
248C LEU* 1.3 61.1 + - - +
249C VAL 4.2 0.4 - - - -
306C TRP* 3.1 20.3 - - - -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 3.4 35.0 - - + +
210C THR* 4.8 2.9 - - + -
234C LEU* 4.4 16.4 - - + +
237C CYS* 3.9 26.7 - - + -
238C ARG 4.7 0.4 - - - +
241C LEU* 4.5 17.7 - - + -
247C GLY* 1.3 73.9 - - - +
249C VAL* 1.3 66.3 + - - +
250C LEU 4.2 0.2 - - - -
266C MSE 3.8 29.9 - - + +
269C THR* 5.1 0.7 - - + -
270C MSE 4.1 17.0 - - - -
304C SER 3.8 1.4 - - - +
305C ARG* 3.3 3.1 - - - -
306C TRP* 2.9 41.0 + - + +
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C HIS* 4.2 28.9 - - + +
122C TRP* 3.7 33.0 - - + -
208C ILE 2.9 9.5 + - - +
209C LEU* 3.4 19.8 - - + -
210C THR* 2.8 35.9 + - - +
248C LEU* 1.3 77.2 - - - +
250C LEU* 1.3 59.3 + - - +
251C THR* 4.3 14.4 - - + -
266C MSE 4.8 0.4 - - - -
304C SER 3.6 5.2 - - - +
305C ARG* 3.8 22.9 - - + -
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C THR* 3.4 13.2 - - + +
212C PRO* 3.7 33.0 - - + -
230C LEU* 4.0 19.3 - - + -
234C LEU* 4.2 16.2 - - + -
249C VAL* 1.3 74.7 - - - +
251C THR* 1.3 70.9 + - - +
252C ALA* 4.9 3.1 - - + -
262C MSE 3.9 39.5 - - + +
265C LEU* 5.5 0.2 - - + -
266C MSE 3.7 14.5 - - + +
303C PHE* 3.1 8.4 - - - +
304C SER* 2.8 42.9 + - - +
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Residues in contact with THR 251 (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 GLN* 3.6 18.6 + - - +
119C HIS* 3.6 35.7 - - + +
210C THR 2.9 6.6 + - - +
211C ASP* 2.7 42.3 + - - +
212C PRO* 3.4 21.1 - - - +
249C VAL* 4.3 9.9 - - + -
250C LEU* 1.3 79.3 - - - +
252C ALA* 1.3 62.6 + - - +
253C TYR* 5.0 0.7 - - - -
302C LEU 3.4 9.2 - - - +
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Residues in contact with ALA 252 (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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211C ASP* 4.3 0.4 + - - -
212C PRO 4.4 4.0 - - - -
226C LEU* 4.3 17.7 - - + -
250C LEU* 4.9 4.7 - - + -
251C THR* 1.3 76.7 - - - +
253C TYR* 1.3 64.2 + - - +
254C SER 4.4 0.3 + - - -
255C ILE* 5.1 5.8 - - + +
262C MSE 4.3 24.0 - - + -
301C SER* 3.5 2.3 - - - -
302C LEU* 2.9 52.7 + - + +
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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