Contacts of the strand formed by residues 120 - 128 (chain G) in PDB entry 3A2C
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 ILE 120 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105G VAL* 4.3 8.1 - - + +
108G HIS* 3.5 43.5 - - + +
109G TRP* 3.6 52.3 - - + +
112G SER* 3.9 11.6 + - - +
118G VAL 3.7 0.6 + - - -
119G ARG* 1.3 84.8 + - - +
121G VAL* 1.3 62.8 + - - +
122G ASP* 4.0 6.1 - - - +
123G VAL* 4.0 23.6 - - + -
136G ILE* 4.2 17.7 - - + -
137G VAL 3.7 9.0 - - - +
138G MET* 4.3 1.8 - - + +
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Residues in contact with VAL 121 (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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63G TYR* 3.4 14.8 - - - +
90G PHE* 3.3 34.3 - - + -
109G TRP* 4.8 5.7 - - - -
119G ARG* 3.6 27.3 + - - +
120G ILE* 1.3 73.8 - - - +
122G ASP* 1.3 82.3 + - - +
137G VAL* 2.6 18.9 + - + +
139G GLU* 3.9 13.7 - - - +
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Residues in contact with ASP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 6.0 0.7 - - - -
53G GLN* 5.4 3.6 - - - +
55G LYS* 2.8 37.2 + - + +
63G TYR* 3.1 24.2 + - - -
109G TRP* 5.4 2.7 - - - -
120G ILE* 4.1 5.8 - - - -
121G VAL* 1.3 87.9 - - - +
123G VAL* 1.3 64.8 - - - +
124G TYR* 3.9 16.7 + - + -
135G LEU 3.8 0.5 - - - +
137G VAL* 2.7 38.7 + - - +
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Residues in contact with VAL 123 (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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52G LEU* 3.6 24.8 - - + +
53G GLN 5.2 1.8 + - - -
54G ILE* 3.4 29.2 - - + -
55G LYS* 2.7 35.2 + - - +
105G VAL* 3.7 22.4 - - + -
120G ILE* 4.0 14.4 - - + -
122G ASP* 1.3 82.8 - - - +
124G TYR* 1.3 68.4 + - - +
134G LEU* 4.5 12.6 - - + -
135G LEU 3.3 8.7 - - - +
136G ILE* 4.6 9.4 - - + -
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Residues in contact with TYR 124 (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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54G ILE* 4.3 0.9 - - - -
55G LYS* 3.4 39.2 - - + +
57G ASN* 3.4 24.5 - - - -
59G ILE* 3.8 31.9 - - + -
62G ASP* 2.6 28.0 + - - +
63G TYR* 3.1 33.0 - + - -
122G ASP* 3.9 15.3 + - - -
123G VAL* 1.3 82.5 - - - +
125G GLU* 1.3 59.8 + - - +
126G ASN* 4.0 12.1 - - - +
133G CYS 3.7 0.2 - - - +
134G LEU* 3.2 5.4 - - - -
135G LEU* 2.6 55.6 + - + -
137G VAL* 4.1 6.1 - - + -
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Residues in contact with GLU 125 (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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51F GLY* 3.6 8.3 + - - -
52F LEU 5.8 0.5 + - - -
54G ILE* 3.8 6.9 - - + +
55G LYS 2.8 8.7 + - - -
56G LYS* 2.8 49.7 + - - +
97G ASP* 3.8 6.5 - - - +
102G ARG* 2.7 39.2 + - - +
124G TYR* 1.3 72.7 - - - +
126G ASN* 1.3 74.8 + - - +
132G LYS* 3.1 36.3 + - + +
133G CYS 3.5 3.6 - - - +
134G LEU* 4.2 3.6 - - + -
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Residues in contact with ASN 126 (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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48F VAL* 3.6 24.2 - - + +
49F LYS 3.3 10.3 - - - +
51F GLY* 4.1 3.6 - - - +
56G LYS 3.5 7.7 + - - -
57G ASN 3.4 18.8 + - - -
58G ALA* 4.4 2.0 - - - -
59G ILE* 3.0 36.3 + - - +
124G TYR* 4.0 7.0 - - - +
125G GLU* 1.3 101.2 + - - +
127G LEU* 1.3 64.0 + - - +
131G ARG 3.7 0.2 - - - +
132G LYS* 3.8 3.0 - - - -
133G CYS* 3.0 35.8 + - - +
135G LEU* 3.7 9.4 - - + +
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Residues in contact with LEU 127 (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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47F HIS 4.2 0.3 - - - +
48F VAL* 3.6 3.8 - - - +
49F LYS* 2.5 61.1 + - + +
50F SER 2.9 28.7 - - - +
51F GLY* 3.6 12.1 - - - -
106F GLU* 4.5 8.1 - - - +
109F TRP* 3.8 15.0 - - + +
110F ARG* 3.9 36.8 - - + -
113F GLN* 4.8 6.3 - - - +
126G ASN* 1.3 72.1 - - - +
128G TYR* 1.3 59.9 + - - +
129G ALA 4.3 0.4 - - - -
130G GLY* 4.5 6.7 - - - +
131G ARG 3.3 9.9 - - - +
132G LYS* 4.3 14.6 - - + -
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Residues in contact with TYR 128 (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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273D PRO* 5.0 6.5 - - + -
47F HIS* 3.6 32.4 - - + +
48F VAL* 4.3 9.2 - - + -
67G SER* 4.9 3.6 + - - -
70G LEU* 3.5 36.2 - - + +
71G GLY* 3.7 21.9 + - - -
74G ILE* 3.8 31.4 - - + -
94G MET* 4.8 6.3 - - + -
126G ASN 3.5 1.2 + - - -
127G LEU* 1.3 73.3 - - - +
129G ALA* 1.3 84.9 + - + +
130G GLY 2.9 0.2 - - - -
131G ARG* 2.7 30.4 + - - +
133G CYS* 3.3 22.2 - - - -
135G LEU* 6.0 0.2 - - + -
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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