Contacts of the strand formed by residues 124 - 130 (chain H) in PDB entry 1I3R
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 THR 124 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G PRO* 6.1 2.9 - - + -
122H GLU 4.8 2.6 + - - -
123H PRO* 1.3 73.2 - - - +
125H VAL* 1.3 62.8 + - - +
126H THR* 4.6 11.1 + - - +
144H SER* 3.4 4.5 + - - +
145H VAL* 3.6 0.5 - - - -
146H SER* 2.9 43.8 + - - +
147H ASP* 4.9 6.1 - - - +
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Residues in contact with VAL 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 3.8 21.2 + - + +
124H THR* 1.3 77.0 - - - +
126H THR* 1.3 70.7 + - - +
143H CYS* 4.0 15.9 - - - -
144H SER 3.2 8.7 - - - +
145H VAL* 4.4 4.0 - - + -
199H CYS* 4.8 1.3 - - - +
201H VAL* 3.9 35.0 - - + -
210H VAL* 4.2 17.3 - - + -
212H VAL* 4.0 29.0 - - + +
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Residues in contact with THR 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO* 5.5 7.1 - - + +
124H THR* 4.6 9.5 + - - +
125H VAL* 1.3 76.1 + - - +
127H VAL* 1.3 92.5 + - - +
128H TYR* 3.7 17.9 - - + -
143H CYS* 3.4 3.6 - - - -
144H SER* 2.8 40.8 + - - +
212H VAL* 5.0 2.9 - - - -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H THR* 1.3 89.1 - - - +
128H TYR* 1.3 72.3 + - - +
141H LEU* 4.9 2.9 - - + -
142H VAL 3.3 10.8 - - - +
143H CYS* 4.3 2.5 - - - -
157H TRP* 3.9 15.9 - - + -
199H CYS* 4.0 16.8 - - + -
212H VAL* 3.4 41.2 - - + +
213H GLU 4.9 0.4 - - - +
214H TRP* 3.5 37.1 - - + -
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Residues in contact with TYR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO* 6.2 3.4 - - + -
182G GLU 6.0 2.0 - - - -
126H THR* 3.7 15.9 - - + -
127H VAL* 1.3 85.7 - - - +
129H PRO* 1.3 82.2 - - + +
130H THR* 3.4 21.5 - - + -
141H LEU* 4.9 3.8 - - - -
142H VAL* 3.0 49.7 + - + +
144H SER* 4.3 20.5 - - - -
184H LEU* 4.3 13.0 - - - +
214H TRP* 4.6 2.5 - - - -
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Residues in contact with PRO 129 (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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128H TYR* 1.3 89.9 - - + +
130H THR* 1.3 72.1 + - - +
140H LEU 3.4 12.6 - - - +
141H LEU* 4.0 14.6 - - + -
191H PRO* 5.6 3.4 - - + -
214H TRP* 3.7 29.2 - - + +
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Residues in contact with THR 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H TYR* 3.4 26.9 - - + -
129H PRO* 1.3 86.4 - - - +
131H LYS* 1.3 74.4 + - - +
132H THR* 3.6 1.9 - - - -
139H ASN* 5.1 2.8 - - - +
140H LEU* 3.2 28.9 + - - +
142H VAL* 3.7 19.4 - - + +
186H MET* 5.5 0.5 - - - +
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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