Contacts of the helix formed by residues 252 - 262 (chain C) in PDB entry 1SMK
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 ASN 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLN 4.3 11.0 + - - +
302A VAL* 3.7 25.5 + - - +
324A SER* 4.1 23.5 - - - -
222C GLY* 5.6 2.9 - - - -
248C ASP* 2.8 32.9 + - - +
249C ARG* 3.8 2.2 - - - +
251C GLN* 1.3 85.2 + - - +
253C GLY* 1.3 54.3 + - - +
254C GLY 3.2 3.1 - - - -
255C THR* 3.0 16.1 + - - +
256C GLU* 2.7 36.0 + - + +
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Residues in contact with GLY 253 (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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196C ARG* 3.7 17.0 - - - -
200C PHE* 5.1 0.9 - - - -
249C ARG 3.1 17.1 + - - -
250C ILE 3.5 5.2 + - - -
252C ASN* 1.3 76.7 - - - +
254C GLY* 1.3 63.3 + - - +
256C GLU* 3.1 8.2 + - - +
257C VAL* 3.0 26.5 + - - +
90D HIS* 3.5 15.7 - - - -
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Residues in contact with GLY 254 (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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124C ARG* 3.8 5.2 - - - -
130C ARG* 3.8 7.8 - - - +
196C ARG* 3.1 14.5 - - - +
250C ILE 5.1 0.2 + - - -
251C GLN 5.2 0.2 + - - -
252C ASN 3.2 0.8 - - - -
253C GLY* 1.3 76.0 - - - +
255C THR* 1.3 63.0 + - - +
257C VAL* 3.1 4.5 + - - +
258C VAL* 3.1 22.7 + - - +
266C SER* 5.3 0.2 - - - -
1313C CIT 3.3 34.6 - - - +
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Residues in contact with THR 255 (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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321A GLU* 5.1 4.0 - - - +
322A VAL 5.3 4.0 - - - +
324A SER* 4.6 4.3 - - - +
124C ARG* 3.2 30.8 + - - +
127C GLY 6.3 0.4 - - - +
128C MET 5.7 0.2 - - - +
130C ARG* 4.5 5.6 + - - +
251C GLN 5.2 0.3 + - - -
252C ASN* 3.0 21.4 + - - +
254C GLY* 1.3 73.5 - - - +
256C GLU* 1.3 65.7 + - - +
258C VAL* 3.0 9.6 + - + +
259C GLU* 2.9 51.9 + - + +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER* 3.7 16.5 + - - +
326A GLY* 3.4 14.2 - - - -
327A PRO* 3.8 11.2 - - + +
249C ARG* 2.6 50.2 + - - +
252C ASN 2.7 16.7 + - - +
253C GLY* 3.2 12.3 - - - +
255C THR* 1.3 74.8 - - - +
257C VAL* 1.3 64.8 + - + +
259C GLU* 3.3 6.5 + - - +
260C ALA* 3.1 21.5 + - + +
86D ALA* 5.0 8.9 - - + +
89D SER* 5.1 1.0 + - - -
90D HIS* 2.8 23.0 + - - +
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Residues in contact with VAL 257 (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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196C ARG* 4.2 7.6 - - - +
253C GLY 3.0 6.0 + - - +
254C GLY 3.6 6.1 - - - +
256C GLU* 1.3 74.5 - - - +
258C VAL* 1.3 63.7 + - - +
260C ALA* 3.2 7.1 + - - +
261C LYS* 3.0 39.9 + - + +
266C SER 4.1 0.2 - - - -
267C ALA* 3.7 32.8 - - + +
83D GLY 4.7 0.7 - - - +
86D ALA* 4.2 3.6 - - + +
87D ASP* 4.0 26.0 - - + +
90D HIS* 3.4 34.3 - - + +
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Residues in contact with VAL 258 (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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321A GLU* 5.3 0.2 - - - +
124C ARG* 4.1 23.1 - - + +
125C LYS 3.8 5.8 - - - +
126C PRO* 3.4 41.5 - - + +
127C GLY 5.1 0.2 - - - +
128C MET 6.0 0.4 - - - +
254C GLY 3.1 14.2 + - - +
255C THR* 3.0 12.0 + - + +
257C VAL* 1.3 75.1 - - - +
259C GLU* 1.3 64.7 + - + +
261C LYS* 3.2 12.0 + - - +
262C ALA 3.2 8.5 + - - -
263C GLY 4.3 0.3 + - - -
265C GLY 4.1 9.3 - - - +
266C SER* 3.4 29.8 - - - -
1313C CIT 3.7 10.1 - - - +
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Residues in contact with GLU 259 (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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321A GLU* 3.6 12.5 - - - +
322A VAL 4.2 1.6 - - - +
323A TYR* 3.4 36.2 - - + +
324A SER* 2.8 48.2 + - - +
126C PRO* 4.5 6.5 - - - +
255C THR* 2.9 37.2 + - + +
256C GLU* 3.5 7.8 - - - +
258C VAL* 1.3 77.7 - - + +
260C ALA* 1.3 62.0 + - - +
262C ALA* 3.1 17.2 + - - +
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Residues in contact with ALA 260 (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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256C GLU* 3.1 12.2 + - + +
257C VAL 3.2 4.2 + - - +
259C GLU* 1.3 77.1 - - - +
261C LYS* 1.3 60.6 + - - +
262C ALA* 3.2 3.9 + - - +
82D PRO* 4.3 11.0 - - + +
83D GLY* 3.4 20.7 + - - +
86D ALA* 3.6 30.7 - - + -
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Residues in contact with LYS 261 (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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257C VAL* 3.0 21.6 + - + +
258C VAL 3.2 1.5 + - - +
260C ALA* 1.3 75.6 - - - +
262C ALA* 1.3 71.8 + - - +
263C GLY 3.4 0.9 - - - -
264C ALA* 3.0 36.5 + - + +
265C GLY 3.3 28.7 - - - +
266C SER 2.7 25.3 + - - +
268C THR* 3.6 10.9 + - - +
58D GLN* 5.2 5.4 + - - -
80D ASN* 5.0 3.8 - - - +
83D GLY* 3.7 31.2 - - - -
84D VAL* 4.6 5.8 - - - +
87D ASP* 2.9 27.5 + - - -
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Residues in contact with ALA 262 (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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126C PRO* 4.1 6.7 - - - -
258C VAL 3.2 3.9 + - - -
259C GLU 3.1 16.1 + - - +
260C ALA 4.5 3.6 - - - +
261C LYS* 1.3 79.8 - - - +
263C GLY* 1.3 58.4 + - - +
264C ALA* 3.4 1.0 + - - +
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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