Contacts of the strand formed by residues 165 - 175 (chain G) in PDB entry 1M06
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 165 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G ASN* 3.9 13.8 + - - +
54G MET* 2.6 45.1 + - - +
90G ALA* 4.4 9.2 - - - -
91G GLY 4.8 2.2 - - - -
163G THR 3.1 4.7 + - - -
164G SER* 1.3 73.7 - - - +
166G ARG* 1.3 61.1 + - - -
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Residues in contact with ARG 166 (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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51G TYR* 3.5 54.1 + - - -
52G ALA* 2.9 46.0 + - - +
53G ASN* 4.1 13.8 - - - +
54G MET* 5.2 0.4 - - - +
88G SER 4.1 0.3 - - - +
89G PHE* 3.7 1.4 - - - +
90G ALA* 2.8 38.8 + - + +
165G GLY* 1.3 73.5 - - - -
167G VAL* 1.3 68.4 + - - +
168G ILE* 4.8 6.7 - - + +
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Residues in contact with VAL 167 (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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24G VAL* 4.8 1.8 - - + -
50G LEU* 4.3 17.9 - - + -
51G TYR* 3.5 2.6 + - - -
52G ALA* 2.9 46.7 + - + +
54G MET* 4.4 19.1 - - + +
64G PHE* 5.7 0.2 - - + -
87G LEU* 4.4 13.2 - - + -
88G SER 3.4 8.7 - - - +
89G PHE* 3.3 44.2 - - + -
166G ARG* 1.3 78.0 - - - +
168G ILE* 1.3 66.8 - - - +
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Residues in contact with ILE 168 (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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50G LEU 3.3 14.4 - - - +
51G TYR* 3.9 26.7 - - + -
86G ASN 4.0 0.2 - - - +
87G LEU* 3.6 4.7 - - - -
88G SER* 2.9 47.8 + - - +
166G ARG* 5.0 7.0 - - + -
167G VAL* 1.3 78.6 - - - +
169G GLY* 1.3 62.7 + - - +
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Residues in contact with GLY 169 (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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49G ASN* 3.8 5.9 + - - +
50G LEU* 2.9 31.1 + - - +
86G ASN* 2.9 13.2 - - - -
87G LEU* 3.9 6.1 - - - -
168G ILE* 1.3 80.6 - - - +
170G THR* 1.3 66.0 + - - -
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Residues in contact with THR 170 (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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47G VAL* 3.8 21.8 - - + -
48G VAL 3.4 12.1 - - - +
49G ASN* 3.6 20.7 + - - +
84G GLY 3.6 1.9 - - - +
85G VAL* 3.3 5.0 - - - -
86G ASN* 2.9 36.1 + - - +
87G LEU* 4.2 0.4 - - - +
169G GLY* 1.3 77.1 + - - -
171G ILE* 1.3 68.8 + - - +
172G ALA* 3.8 4.3 - - + +
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Residues in contact with ILE 171 (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 ALA 4.0 0.9 - - - +
47G VAL* 3.8 0.7 + - - -
48G VAL* 2.8 39.5 + - + +
50G LEU* 4.6 10.1 - - + -
64G PHE* 5.8 1.6 - - + -
66G VAL* 3.7 36.3 - - + -
84G GLY 3.9 2.2 - - - -
85G VAL* 3.4 20.2 - - + -
87G LEU* 3.7 36.8 - - + -
97G VAL* 5.9 0.4 - - + -
155G VAL* 3.0 38.8 - - + -
157G CYS* 6.1 1.1 - - + -
170G THR* 1.3 78.1 - - - +
172G ALA* 1.3 58.8 + - - +
173G THR* 4.5 3.6 - - + +
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Residues in contact with ALA 172 (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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9G HIS* 3.8 9.9 - - - +
11G THR* 3.7 32.3 - - + +
46G ALA 3.2 8.1 - - - +
47G VAL* 4.2 7.6 - - + +
83G ALA* 3.2 2.9 - - - +
84G GLY 2.7 39.5 + - - +
170G THR* 5.1 4.0 - - + -
171G ILE* 1.3 74.8 - - - +
173G THR* 1.3 68.1 + - - +
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Residues in contact with THR 173 (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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9G HIS* 3.9 2.0 - - - -
44G GLU* 3.6 6.1 + - - -
46G ALA* 2.8 25.9 + - + +
66G VAL* 5.1 7.0 - - + +
67G ALA 5.7 0.2 - - - -
68G MET* 2.8 52.5 - - + +
81G ILE* 4.4 7.6 - - - +
82G SER 3.3 12.3 + - - -
83G ALA* 4.1 8.9 - - - +
99G ILE* 5.9 0.3 - - - +
154G GLY* 4.5 10.0 - - - -
155G VAL* 4.5 15.5 - - + -
171G ILE* 4.5 6.1 - - + +
172G ALA* 1.3 80.2 - - - +
174G THR* 1.3 64.4 + - - +
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Residues in contact with THR 174 (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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9G HIS* 3.6 9.4 - - + -
10G ASP* 3.3 26.2 + - - +
11G THR* 5.7 0.2 - - + -
12G ALA 4.1 9.2 - - - +
44G GLU* 2.7 16.6 - - - -
45G ARG* 3.3 26.6 + - - +
46G ALA 4.5 1.3 - - - +
68G MET* 4.3 0.2 - - - -
81G ILE* 3.4 4.3 - - - -
82G SER* 2.7 51.4 + - - +
173G THR* 1.3 82.0 + - - +
175G GLN* 1.3 63.0 + - - +
176G VAL* 3.8 6.1 + - - +
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Residues in contact with GLN 175 (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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43G ALA 4.8 2.8 - - - +
44G GLU* 2.6 41.6 + - + +
45G ARG* 4.8 6.4 + - - -
70G VAL* 3.3 11.8 - - + +
71G ASP* 2.7 50.4 + - - +
74G PRO* 4.9 0.2 - - - +
79G CYS* 3.2 24.9 - - - -
80G VAL 3.6 5.6 - - - +
81G ILE* 4.2 14.4 - - + -
142G ILE* 4.2 3.8 - - - +
174G THR* 1.3 75.5 + - - +
176G VAL* 1.3 59.5 + - - +
177G ILE* 3.2 32.8 + - + +
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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