Contacts of the strand formed by residues 135 - 140 (chain H) in PDB entry 5T0G
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 LEU 135 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35H SER* 3.8 39.9 - - - +
36H VAL 4.7 7.9 - - - +
37H GLY* 4.9 1.8 - - - +
46H LEU* 4.2 6.8 - - + +
74H LEU* 3.4 6.3 - - - +
75H VAL* 3.3 42.3 + - + +
76H TYR* 5.3 1.1 - - - +
77H SER* 5.2 0.7 - - - +
133H SER* 4.5 7.6 - - - +
134H LEU* 1.3 83.9 - - - +
136H ILE* 1.3 62.4 + - - +
146H LEU* 5.0 9.0 - - + -
147H PHE 3.4 4.5 - - - +
148H GLN* 3.6 33.0 - - + +
161H THR* 4.2 17.5 - - + -
163H MET* 5.1 11.4 - - + +
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE* 4.8 7.0 - - + -
73H GLY 4.6 2.7 - - - +
74H LEU* 3.6 29.4 - - + -
107H THR* 4.8 6.3 - - - +
110H LEU* 5.2 9.9 - - + -
111H VAL* 3.7 39.5 - - + +
114H VAL* 5.7 5.8 - - + -
134H LEU* 4.2 19.5 - - + -
135H LEU* 1.3 75.0 - - - +
137H CYS* 1.3 72.7 + - - +
146H LEU* 3.3 6.2 - - - +
147H PHE* 2.7 48.8 + - + +
148H GLN 6.2 0.2 - - - -
149H SER* 5.1 7.9 - - - +
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Residues in contact with CYS 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H VAL* 3.6 28.0 - - + -
46H LEU* 3.4 29.4 - - - -
72H ILE* 3.2 22.7 - - - +
73H GLY* 3.4 23.3 + - - -
107H THR* 3.4 10.0 - - - +
136H ILE* 1.3 78.3 - - - +
138H GLY* 1.3 60.9 + - - +
145H TYR 3.3 10.8 - - - +
146H LEU* 4.2 2.9 - - + -
147H PHE* 5.9 0.7 - - - -
213H CYS* 3.8 14.4 - - - -
218H PHE* 5.5 2.5 - - - -
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Residues in contact with GLY 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H VAL* 4.4 0.9 - - - +
71H HIS 3.5 16.2 - - - -
72H ILE* 4.3 0.9 - - - -
107H THR* 3.6 12.1 - - - -
137H CYS* 1.3 82.1 - - - +
139H TRP* 1.3 59.0 + - - -
144H PRO* 3.3 5.2 - - - +
145H TYR* 2.9 26.7 + - - +
213H CYS* 3.6 14.1 - - - +
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Residues in contact with TRP 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H HIS* 3.5 32.9 + - + +
107H THR* 4.3 0.4 - - - +
138H GLY* 1.3 73.7 - - - +
140H ASN* 1.3 60.4 + - - +
144H PRO* 3.8 10.1 - - + -
213H CYS* 4.8 2.4 - - + +
214H ASN 3.8 21.1 - - - +
215H GLU* 3.2 37.7 - - - +
217H GLY* 5.5 1.6 - - - +
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Residues in contact with ASN 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H HIS* 5.6 2.9 - - + -
105H ILE 5.7 0.7 - - - +
106H PRO* 4.8 11.4 - - + -
107H THR* 4.6 17.5 - - + +
138H GLY 4.2 0.4 - - - -
139H TRP* 1.3 75.6 - - - +
141H GLU* 1.3 69.7 + - + +
142H GLY 3.1 1.6 - - - -
143H ARG* 2.9 24.1 + - - +
145H TYR* 3.5 21.9 + - + -
215H GLU* 4.0 0.8 + - - -
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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