Contacts of the helix formed by residues 246 - 259 (chain A) in PDB entry 1XSK
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 THR 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLY* 4.8 0.9 - - - -
244A GLY 3.3 1.0 - - - -
245A PRO* 1.3 91.9 - - + +
247A PRO* 1.3 75.2 - - + +
248A LYS* 3.8 1.9 + - - -
249A ALA* 2.8 19.8 + - - +
250A VAL* 2.9 16.9 + - - +
596A PRO* 4.6 15.9 - - + -
3013A SO4 3.0 39.3 + - - +
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Residues in contact with PRO 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A MET* 3.2 34.6 - - + +
202A THR 4.6 6.5 - - - +
203A ASN* 5.4 2.5 - - - -
205A GLY* 5.1 4.5 - - - +
245A PRO 4.5 2.0 - - - +
246A THR* 1.3 86.5 - - - +
248A LYS* 1.3 61.8 + - - +
250A VAL* 3.4 1.1 + - + -
251A LEU* 3.1 26.3 + - - +
502A LEU* 5.7 0.2 - - + -
592A MET* 4.1 24.7 - - + +
593A MET* 4.1 24.5 - - + +
596A PRO* 3.6 26.7 - - + -
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A THR* 3.2 2.0 + - - -
247A PRO* 1.3 77.1 - - - +
249A ALA* 1.3 57.7 + - - +
251A LEU* 3.6 8.5 + - - +
252A ASP* 2.9 28.8 + - - +
583A ARG* 3.5 20.1 + - - +
585A THR* 4.0 22.6 + - + +
589A ARG* 3.8 6.0 - - - +
593A MET* 4.0 31.0 - - + +
594A GLU* 3.1 43.0 + - - +
612A ASP* 3.6 15.4 + - - -
3013A SO4 3.7 28.7 + - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP 4.3 2.5 - - - -
244A GLY 3.3 27.1 - - - +
245A PRO* 4.2 1.6 - - + -
246A THR* 2.8 23.0 + - - +
248A LYS* 1.3 78.2 - - - +
250A VAL* 1.3 65.0 + - - +
252A ASP* 3.2 4.5 + - - +
253A ARG* 3.0 28.9 + - - +
583A ARG* 3.7 10.5 - - - +
3013A SO4 4.0 5.4 - - - +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.9 23.8 - - + -
201A MET* 4.0 12.6 - - + -
205A GLY 3.6 19.7 - - - +
206A TYR* 3.8 5.8 - - - +
207A GLY* 3.7 20.4 - - - +
242A ILE* 3.8 10.3 - - + +
243A ASP 3.9 7.2 - - - -
244A GLY* 3.5 18.2 - - - +
246A THR 2.9 19.5 + - - +
247A PRO 3.5 7.0 - - - +
248A LYS 3.3 0.2 - - - -
249A ALA* 1.3 75.9 - - - +
251A LEU* 1.3 51.3 + - - +
253A ARG* 3.1 4.5 + - - +
254A TYR* 2.7 35.9 + - - +
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 4.3 13.2 - - + -
201A MET* 4.2 10.8 - - - -
247A PRO 3.1 17.6 + - - +
248A LYS* 3.9 6.7 - - - +
250A VAL* 1.3 78.9 - - - +
252A ASP* 1.3 55.3 + - - +
254A TYR* 4.0 5.6 - - + -
255A THR* 2.7 39.2 + - + +
501A GLY 3.7 15.3 - - - +
502A LEU* 3.9 12.8 - - - +
504A GLY* 3.7 32.3 - - - +
583A ARG 3.9 2.9 - - - +
584A GLY 4.1 10.8 - - - +
585A THR* 5.4 0.9 - - - -
586A PRO* 4.2 8.3 - - + -
593A MET* 3.7 28.3 - - + -
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LYS 2.9 19.1 + - - +
249A ALA* 3.3 9.1 - - - +
250A VAL 3.2 0.2 - - - -
251A LEU* 1.3 76.7 - - - +
253A ARG* 1.3 62.8 + - - +
256A ARG* 3.0 16.4 + - - +
260A ARG* 2.8 50.9 + - - +
582A ALA 4.1 0.2 - - - +
583A ARG* 3.0 47.3 + - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 5.6 0.6 - - + +
62A GLU* 3.4 47.7 + - - +
63A GLY* 3.9 17.2 - - - -
64A ILE* 4.3 7.3 - - + +
242A ILE* 3.5 17.9 - - + -
243A ASP* 2.5 43.9 + - - -
244A GLY* 2.7 21.8 + - - -
249A ALA* 3.0 16.9 + - - +
250A VAL 3.6 1.6 - - - +
252A ASP* 1.3 74.5 - - + +
254A TYR* 1.3 67.6 + - - +
256A ARG* 3.1 11.1 + - - +
257A PHE* 2.8 26.1 + - - +
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 3.5 23.0 - - - +
199A PHE* 3.7 43.5 - + + +
209A LEU* 4.3 10.1 - - + -
242A ILE* 3.9 20.1 - - + +
250A VAL 2.7 22.1 + - - +
251A LEU* 3.6 11.4 - - + +
253A ARG* 1.3 73.1 - - - +
255A THR* 1.3 68.2 + - + +
257A PHE* 3.3 6.9 + + - +
258A THR* 2.8 61.7 + - + -
470A VAL* 4.0 14.6 - - - +
473A GLN* 4.2 8.1 + - - -
503A SER 3.6 21.6 + - - -
504A GLY* 4.1 9.0 - - - -
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Residues in contact with THR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LEU* 2.7 24.5 + - - +
254A TYR* 1.3 74.1 - - + +
256A ARG* 1.3 60.1 + - - +
257A PHE 3.1 2.0 - - - -
258A THR* 4.1 2.9 - - - -
259A GLY* 2.6 50.7 + - - +
260A ARG* 2.7 34.4 + - - -
261A PRO* 4.2 2.0 - - + -
473A GLN* 4.7 0.4 - - - +
504A GLY* 3.9 31.0 - - - +
584A GLY* 3.5 24.7 - - - +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.9 26.4 + - - +
85A ASN* 2.9 25.3 + - - +
252A ASP* 3.0 22.6 + - - +
253A ARG* 3.5 9.8 - - - +
255A THR* 1.3 78.3 + - - +
257A PHE* 1.3 58.9 - - - +
260A ARG* 3.5 38.1 - - - +
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Residues in contact with PHE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 3.5 30.1 - - + -
61A GLN* 3.9 11.6 - - + +
64A ILE* 3.7 20.0 - - + -
84A LEU* 3.6 35.5 - - + -
85A ASN* 2.9 60.9 + - - +
86A ILE* 4.3 1.6 - - + -
209A LEU* 4.1 9.4 - - + -
240A PHE* 3.7 33.4 - + + -
242A ILE* 4.9 8.5 - - + -
253A ARG 2.8 15.9 + - - +
254A TYR* 3.3 4.5 - - - +
256A ARG* 1.3 77.6 - - - +
258A THR* 1.3 67.9 + - + +
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Residues in contact with THR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 3.7 15.4 - - - +
84A LEU* 4.1 9.4 - - + -
85A ASN* 4.1 3.8 + - - -
209A LEU* 4.0 15.0 - - + -
254A TYR* 2.8 49.1 + - + +
257A PHE* 1.3 81.5 - - + +
259A GLY* 1.3 55.2 + - - +
470A VAL* 3.8 28.7 - - + -
471A GLY* 3.6 16.6 - - - -
473A GLN* 3.0 23.0 + - - -
474A LYS* 4.6 4.0 + - - +
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 4.1 6.8 - - - +
255A THR* 2.6 29.7 + - - +
257A PHE 3.7 0.8 - - - -
258A THR* 1.3 76.4 + - - +
260A ARG* 1.3 62.1 + - - -
473A GLN* 3.0 24.5 + - - +
474A LYS* 3.8 19.5 - - - -
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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