Contacts of the strand formed by residues 133 - 140 (chain I) in PDB entry 5T0J
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 133 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28I ILE* 3.2 41.6 - - - +
75I SER 4.0 0.7 - - - +
77I ALA* 2.9 35.7 + - - +
118I LYS* 4.6 4.9 + - - +
131I GLY 4.2 1.0 + - - -
132I VAL* 1.3 71.0 + - - +
134I LEU* 1.3 60.2 + - - +
135I LEU* 5.8 0.7 - - - +
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I LEU* 5.6 0.7 - - + -
74I CYS* 3.8 18.6 - - + -
75I SER 3.1 13.5 - - - +
76I VAL* 4.1 12.1 - - + +
83I ALA* 5.5 4.9 - - + +
86I LEU* 4.2 32.1 - - + -
87I THR* 5.9 2.2 - - + +
90I LEU* 5.6 0.2 - - + -
114I LEU* 4.2 12.6 - - + -
118I LYS* 5.2 5.0 - - - +
132I VAL* 4.0 11.1 + - + +
133I SER* 1.3 75.1 - - - +
135I LEU* 1.3 84.7 + - - +
136I TYR* 3.4 44.0 - - + +
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I CYS* 4.0 29.6 - - + -
35I LEU 4.0 20.2 - - - +
36I GLY* 5.7 0.9 - - - -
45I LEU* 4.1 19.5 - - + -
74I CYS* 3.2 23.8 - - - +
75I SER* 3.0 23.5 + - - +
133I SER 5.8 0.9 - - - +
134I LEU* 1.3 77.9 - - - +
136I TYR* 1.3 73.3 + - - +
137I ILE* 5.7 0.2 - - + -
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Residues in contact with TYR 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I LEU* 4.7 13.0 - - + -
73I ALA 3.9 4.3 - - - -
90I LEU* 3.6 22.7 - - + -
107I CYS* 5.9 2.9 - - + -
110I LEU* 5.5 4.3 - - + -
111I VAL* 3.5 50.9 + - + +
114I LEU* 3.2 29.8 - - - +
115I CYS* 5.0 6.5 - - - -
118I LYS* 5.4 2.6 + - - +
134I LEU* 3.4 36.6 - - + +
135I LEU* 1.3 83.0 - - - +
137I ILE* 1.3 71.0 + - - +
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Residues in contact with ILE 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL* 4.3 31.6 - - + -
45I LEU* 3.6 44.6 - - + -
71I ASP 5.2 0.9 - - - +
72I MET* 3.3 27.5 - - - +
73I ALA* 3.3 38.3 + - + +
107I CYS* 6.0 2.5 - - - -
135I LEU* 5.7 0.9 - - + -
136I TYR* 1.3 82.0 - - - +
138I GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL* 5.4 3.4 - - - +
71I ASP 3.6 9.4 - - - -
72I MET* 3.6 16.2 - - - -
107I CYS* 5.0 7.9 - - - -
137I ILE* 1.3 78.9 - - - +
139I TRP* 1.3 60.4 + - - +
144I GLY 3.9 0.8 - - - +
145I PHE* 3.5 27.3 - - - +
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Residues in contact with TRP 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I ASP* 4.2 17.0 + - + +
72I MET* 4.5 6.3 - - - +
104I PRO* 6.1 1.4 - - - +
107I CYS* 4.9 5.3 - - - -
138I GLY* 1.3 74.9 - - - +
140I ASP* 1.3 88.3 + - - +
141I LYS* 3.8 25.1 - - + -
144I GLY* 3.3 24.2 - - - -
145I PHE* 3.3 37.4 - + + -
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Residues in contact with ASP 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I PRO* 4.9 12.5 - - + +
107I CYS* 4.6 12.8 - - - -
108I GLU* 2.8 32.0 - - - +
139I TRP* 1.3 100.8 - - - +
141I LYS* 1.3 61.8 + - - +
142I HIS* 3.4 12.3 + - + +
143I TYR* 3.0 16.7 + - - +
144I GLY 2.5 46.9 + - - +
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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