Contacts of the strand formed by residues 118 - 124 (chain M) in PDB entry 4UJ3
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 118 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85M VAL 3.0 7.8 + - - +
86M GLY* 3.0 3.6 - - - -
87M ALA 2.7 32.7 + - - +
116M ASN 4.3 6.5 - - - +
117M ILE* 1.3 71.4 - - - +
119M ILE* 1.3 59.4 + - - +
149M SER* 5.0 0.7 - - - +
168M ILE* 3.5 25.6 - - + +
171M GLU* 3.5 31.0 - - + +
172M ILE* 3.3 39.5 - - + +
175M ILE* 4.6 11.0 - - + -
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Residues in contact with ILE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ALA* 3.4 9.6 - - + +
89M LEU* 4.3 11.9 - - + -
106M LEU* 3.9 17.3 - - + -
109M LEU* 3.3 39.5 - - + -
117M ILE* 3.3 27.2 + - + +
118M VAL* 1.3 78.1 - - - +
120M MET* 1.3 68.3 + - - +
147M GLY 4.7 1.5 + - - +
148M LEU* 3.4 30.4 - - + -
149M SER* 3.4 21.5 + - - -
168M ILE* 4.6 0.9 - - - -
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Residues in contact with MET 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ALA 2.8 10.5 + - - -
88M LEU* 3.3 34.5 - - + -
89M LEU* 2.8 32.1 + - - +
119M ILE* 1.3 76.9 - - - +
121M LEU* 1.3 64.9 + - - +
122M VAL* 3.8 6.2 + - + +
149M SER* 3.3 32.8 - - - +
150M PHE* 4.2 1.6 - - - +
151M ILE* 3.6 17.5 - - + -
164M ALA* 3.1 51.6 - - + +
167M THR* 4.4 10.5 - - - -
168M ILE* 3.9 13.8 - - + +
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Residues in contact with LEU 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M LEU* 3.3 28.5 - - + +
91M TYR* 3.9 27.6 - - + -
99M TYR* 4.8 6.5 - - + -
102M VAL* 4.0 22.2 - - + -
119M ILE 4.3 0.4 + - - -
120M MET* 1.3 72.0 - - - +
122M VAL* 1.3 60.5 + - - +
139M ALA 4.4 7.4 - - - +
142M PHE* 4.2 24.5 - - + -
143M ALA* 4.4 5.4 - - + -
148M LEU* 4.5 14.0 - - + +
149M SER 3.1 12.2 + - - +
150M PHE* 3.4 23.7 - - + -
151M ILE 3.2 26.3 + - - +
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Residues in contact with VAL 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LEU* 4.6 7.0 - - + -
88M LEU* 4.4 12.6 - - + -
89M LEU 2.9 6.7 + - - +
90M VAL* 2.7 20.3 - - + +
91M TYR* 2.5 33.1 + - - -
120M MET* 3.8 33.2 - - + +
121M LEU* 1.3 78.8 - - - +
123M GLY* 1.3 64.1 + - - +
124M ASN* 3.5 5.4 - - + +
151M ILE* 3.5 5.4 - - + +
153M THR* 3.2 39.7 - - + +
164M ALA* 5.0 1.6 - - + -
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Residues in contact with GLY 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M TYR* 3.2 32.6 + - - -
93M ILE* 3.9 6.8 - - - +
122M VAL* 1.3 77.6 + - - -
124M ASN* 1.3 56.6 + - - +
126M SER* 4.5 0.2 - - - -
150M PHE* 4.7 0.7 - - - -
151M ILE 3.4 10.8 - - - -
152M GLU* 2.9 13.8 - - - +
153M THR 2.6 27.9 + - - +
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Residues in contact with ASN 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M VAL 3.0 26.7 + - - +
23M GLY* 3.7 11.5 + - - -
27M LEU* 3.9 9.3 - - + +
90M VAL* 4.1 11.4 - - + -
91M TYR 3.2 9.8 + - - +
93M ILE* 2.9 34.4 + - - +
122M VAL* 4.3 2.0 - - + -
123M GLY* 1.3 78.5 - - - +
125M LYS* 1.3 74.7 + - - +
126M SER 3.3 2.0 - - - -
153M THR* 2.8 28.1 + - - +
155M ALA* 3.3 15.3 + - - +
200M GNP 3.4 23.2 + - - -
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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