Contacts of the strand formed by residues 245 - 251 (chain G) in PDB entry 6S1M
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 245 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G THR* 2.9 9.6 + - - -
53G ARG* 3.8 26.6 + - - +
240G LYS* 4.0 6.1 - - - +
241G ILE* 2.8 23.5 + - - +
243G ASP 3.7 1.0 + - - +
244G MET* 1.3 83.9 - - - +
246G HIS* 1.3 67.2 + - - +
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Residues in contact with HIS 246 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49G GLN* 2.6 24.3 + - - -
50G LEU* 3.2 7.6 - - - +
51G THR* 2.8 54.8 + - + -
53G ARG* 4.0 14.0 + - - -
238G GLU* 3.5 12.5 + - - +
239G TYR 3.4 14.6 - - - +
240G LYS* 4.0 12.2 + - + -
241G ILE* 3.7 9.8 - - - +
245G GLY* 1.3 77.4 - - - +
247G LEU* 1.3 62.0 + - - +
248G LYS* 3.1 47.1 - - + -
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Residues in contact with LEU 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 5.0 5.8 - - - +
18G ALA* 4.0 10.8 - - + -
19G LEU* 4.1 7.4 - - + -
48G VAL* 3.7 28.3 - - + -
49G GLN 3.4 2.0 - - - +
50G LEU* 3.8 27.8 - - + -
218G ALA* 4.0 4.7 - - + -
221G LEU* 3.5 28.9 - - + -
237G VAL 4.0 1.0 - - - +
238G GLU* 3.5 1.9 - - - -
239G TYR* 2.9 39.2 + - + +
241G ILE* 4.3 5.6 - - + -
246G HIS* 1.3 78.9 - - - +
248G LYS* 1.3 60.9 + - - +
249G TYR* 3.7 27.6 - - + +
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Residues in contact with LYS 248 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47G LEU 3.5 1.0 - - - +
48G VAL* 3.2 6.1 - - - +
49G GLN* 2.7 55.4 + - + +
236G VAL* 4.6 9.4 - - + -
237G VAL 3.5 3.8 - - - +
238G GLU* 3.0 42.8 - - + -
246G HIS* 3.1 31.4 + - + +
247G LEU* 1.3 71.5 - - - +
249G TYR* 1.3 62.9 + - - +
250G TYR* 4.1 26.6 + - + +
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Residues in contact with TYR 249 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G ALA* 2.8 40.9 + - - +
19G LEU* 4.8 0.4 - - + +
22G LEU* 3.9 15.3 - - + -
47G LEU 3.4 2.5 - - - -
48G VAL* 3.8 29.2 - - + -
214G PHE 4.5 0.3 + - - -
215G PHE* 3.4 68.9 + + + -
218G ALA* 3.7 14.6 - - + +
235G LEU 3.5 1.9 - - - +
236G VAL* 3.6 1.4 - - - -
237G VAL* 2.7 49.8 + - + +
239G TYR* 3.9 12.3 - + - -
247G LEU* 3.7 15.9 - - + +
248G LYS* 1.3 75.7 - - - +
250G TYR* 1.3 63.7 + - - +
251G LEU 4.0 0.2 + - - -
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Residues in contact with TYR 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G SER* 2.8 25.4 - - - -
47G LEU* 2.7 51.1 + - + +
49G GLN* 4.4 9.6 - - + +
128G ILE* 3.5 41.5 - - + +
133G TYR* 4.1 8.1 - - - -
215G PHE* 4.5 0.4 - - - -
234G PRO* 4.4 17.0 - - + -
235G LEU 3.3 6.1 - - - +
236G VAL* 3.6 35.5 - - + +
248G LYS* 4.1 32.4 + - + +
249G TYR* 1.3 74.6 - - - +
251G LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 3.5 33.7 - - + +
46G SER* 4.2 6.3 - - - -
207G PHE* 3.5 24.9 - - + -
208G ALA* 4.1 6.5 - - + +
211G TYR* 3.8 26.0 - - + -
212G LEU* 3.7 33.9 - - + -
215G PHE* 3.6 16.4 - - + -
234G PRO* 3.1 4.5 - - - +
235G LEU* 2.9 36.6 + - + +
249G TYR 4.0 0.8 + - - -
250G TYR* 1.3 74.8 - - - +
252G ALA* 1.3 72.8 + - - +
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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