Contacts of the strand formed by residues 131 - 141 (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 VAL 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ASN* 5.3 2.0 - - + +
87G LEU 2.8 26.7 - - - +
88G SER* 4.2 9.4 - - - +
95G PRO* 4.0 4.7 - - - +
126G VAL* 3.5 17.1 - - + +
128G SER* 2.8 48.0 + - - +
130G GLY* 1.3 76.7 - - - +
132G CYS* 1.3 68.0 + - - +
133G SER* 5.2 2.2 - - - -
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Residues in contact with CYS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL* 4.0 2.3 - - - +
86G ASN* 3.7 1.2 + - - -
87G LEU* 3.0 48.2 + - - +
95G PRO* 3.1 35.3 - - + +
97G VAL* 3.8 23.8 - - - -
124G MET* 3.6 21.5 - - + -
126G VAL 3.2 5.6 - - - +
127G GLY* 4.9 0.7 - - - -
131G VAL* 1.3 73.8 - - - +
133G SER* 1.3 62.6 + - - +
157G CYS* 4.6 0.2 - - - -
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Residues in contact with SER 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL* 3.2 7.2 + - - -
86G ASN* 2.9 25.1 + - - -
124G MET* 3.6 2.6 - - - +
125G SER* 2.8 33.0 + - - -
126G VAL* 3.0 32.4 + - - +
131G VAL* 5.2 2.7 - - - -
132G CYS* 1.3 74.2 - - - +
134G ALA* 1.3 66.1 + - - +
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Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ALA 4.4 1.1 - - - -
84G GLY* 3.3 1.6 - - - -
85G VAL* 2.7 40.5 + - + +
97G VAL* 3.9 25.8 - - + -
122G ILE* 4.3 10.1 - - + -
123G GLU 3.6 17.0 - - - +
124G MET* 3.9 3.1 - - - -
125G SER* 3.9 9.4 - - - +
133G SER* 1.3 83.2 + - - +
135G ARG* 1.3 61.9 + - - +
136G ASP 4.2 0.2 - - - -
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Residues in contact with ARG 135 (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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7G THR* 3.5 19.2 + - - +
8G LYS* 4.2 14.6 - - + +
9G HIS* 2.8 54.6 + - + +
10G ASP* 4.6 7.5 + - - +
11G THR* 5.0 4.4 + - - +
83G ALA 3.3 6.3 - - - +
84G GLY* 4.5 3.1 - - - -
123G GLU* 4.4 4.4 + - - +
125G SER* 5.2 2.4 - - - -
134G ALA* 1.3 76.8 - - - +
136G ASP* 1.3 62.9 + - - +
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LYS* 3.9 29.4 + - - +
9G HIS* 4.7 0.2 - - - +
82G SER* 3.3 3.1 - - - -
83G ALA* 2.8 31.3 + - - +
99G ILE* 4.9 0.7 - - - +
122G ILE* 3.8 26.0 - - + +
123G GLU* 3.0 41.3 + - - +
134G ALA 4.2 0.2 - - - -
135G ARG* 1.3 75.2 - - - +
137G CYS* 1.3 92.9 + - - +
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Residues in contact with CYS 137 (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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8G LYS* 3.7 21.8 - - - -
80G VAL* 3.6 19.7 - - + -
81G ILE 3.2 15.5 - - - +
82G SER* 3.5 14.4 - - - -
99G ILE* 5.0 1.1 - - - -
121G PRO 5.3 0.7 - - - +
122G ILE* 4.3 8.3 - - - +
136G ASP* 1.3 104.6 + - - +
138G ALA* 1.3 65.3 + - - +
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Residues in contact with ALA 138 (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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80G VAL* 3.6 4.5 - - - -
81G ILE 2.9 31.1 + - - +
99G ILE* 4.5 10.8 - - + -
120G TYR* 4.0 30.7 - - + -
121G PRO 5.1 3.4 - - - +
122G ILE* 4.8 4.0 - - + -
137G CYS* 1.3 79.7 - - - +
139G THR* 1.3 63.5 + - - +
140G VAL* 3.7 6.2 - - + +
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Residues in contact with THR 139 (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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78G ASN* 4.2 25.1 - - + +
79G CYS* 4.2 9.9 - - - +
80G VAL* 4.6 4.6 - - + +
120G TYR* 3.7 18.9 - - - -
138G ALA* 1.3 70.4 - - - +
140G VAL* 1.3 68.9 + - - +
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Residues in contact with VAL 140 (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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78G ASN* 2.9 14.8 - - - +
79G CYS 3.3 16.4 + - - +
81G ILE* 3.4 36.1 - - + -
99G ILE* 5.1 4.3 - - + -
100G VAL 6.5 0.2 - - - -
101G ARG* 3.4 35.7 - - + -
120G TYR* 4.0 27.8 - - + +
138G ALA* 3.7 12.1 - - + +
139G THR* 1.3 81.7 - - - +
141G ASP* 1.3 70.1 + - - +
142G ILE* 3.2 5.4 + - + +
153G VAL* 4.6 2.5 - - + -
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Residues in contact with ASP 141 (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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77G PRO 3.8 3.6 - - - +
78G ASN* 3.1 25.3 - - - +
101G ARG* 2.8 28.9 + - - -
120G TYR* 4.5 1.7 + - - -
140G VAL* 1.3 72.7 - - - +
142G ILE* 1.3 59.5 + - - +
143G HIS* 3.7 8.9 - - - +
145G ARG* 2.5 49.2 + - - +
151G VAL* 4.9 0.7 - - - +
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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