Contacts of the strand formed by residues 46 - 53 (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 SER 46 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G LEU* 4.1 5.9 - - - +
40G MET* 3.1 10.2 - - - +
41G ASP* 2.6 49.3 + - - +
44G HIS 3.5 0.4 - - - -
45G VAL* 1.3 81.7 - - - +
47G LEU* 1.3 60.5 + - - +
48G VAL* 5.6 0.2 - - - -
211G TYR* 4.5 2.6 - - - -
215G PHE* 3.8 29.1 - - - -
250G TYR 2.8 18.6 - - - -
251G LEU* 4.2 5.2 - - - -
252G ALA 4.8 0.2 - - - +
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Residues in contact with LEU 47 (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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38G GLN* 4.0 22.9 - - + +
39G SER* 3.5 26.0 - - - +
40G MET* 3.8 16.4 - - + +
46G SER* 1.3 76.0 - - - +
48G VAL* 1.3 62.6 + - - +
49G GLN* 5.4 0.2 - - + -
126G LEU* 4.1 23.3 - - + -
128G ILE* 3.4 32.8 - - + -
249G TYR* 3.4 2.3 - - - -
250G TYR* 2.7 58.6 + - + -
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Residues in contact with VAL 48 (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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19G LEU* 3.3 27.8 - - + -
22G LEU* 3.7 28.3 - - + -
23G ILE* 3.6 26.9 - - + -
37G LEU* 3.5 3.6 - - + +
38G GLN* 3.1 9.2 - - - +
39G SER 2.9 33.2 + - - +
41G ASP 5.6 1.1 - - - +
46G SER* 5.3 0.7 - - - +
47G LEU* 1.3 77.9 - - - +
49G GLN* 1.3 63.0 + - - +
50G LEU 4.1 1.1 - - - +
247G LEU* 3.7 16.6 - - + -
248G LYS 3.2 6.3 - - - +
249G TYR* 3.8 12.8 - - + -
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Residues in contact with GLN 49 (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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36G ASN* 3.3 15.0 + - - +
37G LEU 3.3 2.9 - - - +
38G GLN* 3.4 29.8 - - + +
47G LEU* 5.4 0.2 - - + -
48G VAL* 1.3 75.5 - - - +
50G LEU* 1.3 75.3 + - - +
51G THR* 2.6 23.6 + - - -
128G ILE* 5.1 5.2 - - + -
246G HIS* 2.6 31.9 + - - +
247G LEU* 3.4 4.9 + - - -
248G LYS* 2.7 54.5 + - + +
250G TYR* 4.4 12.6 - - + -
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Residues in contact with LEU 50 (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* 3.6 28.5 - - + -
19G LEU* 4.3 7.0 - - + -
28G TRP* 4.0 25.6 - - + -
35G VAL* 5.5 1.3 - - + -
36G ASN* 3.4 5.3 - - - -
37G LEU* 2.7 49.5 + - + +
48G VAL* 4.1 0.8 - - - +
49G GLN* 1.3 83.1 + - - +
51G THR* 1.3 62.1 + - - +
52G LEU* 4.1 19.5 - - + +
241G ILE* 3.8 17.5 - - + -
246G HIS 3.2 17.3 - - - +
247G LEU* 3.8 20.2 - - + +
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Residues in contact with THR 51 (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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35G VAL 4.0 3.1 - - - +
36G ASN* 3.5 8.7 + - - +
49G GLN* 2.6 26.7 + - - -
50G LEU* 1.3 71.0 - - - +
52G LEU* 1.3 67.8 + - - +
53G ARG* 3.9 31.9 - - + +
245G GLY* 2.9 9.9 - - - -
246G HIS* 2.8 60.2 + - + +
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Residues in contact with LEU 52 (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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6G LEU* 5.9 1.8 - - + -
11G ILE* 5.1 5.4 - - + -
12G LEU* 4.6 14.8 - - + -
15G VAL* 4.9 5.8 - - + -
28G TRP* 4.5 14.1 - - + -
34G GLY* 3.2 1.3 - - - -
35G VAL* 2.8 49.6 + - + +
50G LEU* 4.1 25.3 - - + -
51G THR* 1.3 80.8 - - - +
53G ARG* 1.3 64.5 + - - +
57G PHE* 3.8 21.7 - - + -
90G LEU* 6.5 0.7 - - + -
241G ILE* 4.0 24.9 - - + -
244G MET* 3.2 27.8 - - + -
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Residues in contact with ARG 53 (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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33G SER 3.7 8.3 - - - +
34G GLY* 4.3 0.4 - - - -
51G THR* 3.9 14.9 - - + +
52G LEU* 1.3 72.7 - - - +
54G SER* 1.3 66.3 + - - +
55G GLU* 4.0 18.6 - - + +
56G GLY* 3.0 17.2 + - - +
57G PHE* 3.4 10.1 - - - -
240G LYS* 4.7 10.1 - - - +
243G ASP* 5.0 8.3 - - - +
244G MET* 2.5 21.4 + - - +
245G GLY* 3.8 17.4 + - - +
246G HIS* 4.0 22.6 + - - -
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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