Contacts of the strand formed by residues 124 - 129 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 5.9 0.3 - - - +
122B GLU 4.2 4.0 + - - -
123B PRO* 1.3 75.2 + - - +
125B VAL* 1.3 65.8 + - - +
126B THR* 4.0 7.2 + - - +
144B SER* 3.5 4.2 + - - +
146B SER* 3.0 40.4 + - - +
147B ASP* 4.7 6.8 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 3.9 7.8 + - + +
124B THR* 1.3 78.6 - - - +
126B THR* 1.3 70.3 + - - +
143B CYS* 4.0 22.2 - - - -
144B SER 3.3 7.9 - - - +
145B VAL* 4.3 9.2 - - + -
199B CYS* 4.8 2.9 - - + +
201B VAL* 3.6 36.3 - - + -
210B VAL* 4.4 15.0 - - + +
212B VAL* 3.5 32.7 - - + +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 5.7 7.2 - - + +
124B THR* 4.7 8.4 + - - +
125B VAL* 1.3 79.4 + - - +
127B VAL* 1.3 74.6 + - - +
128B TYR* 3.7 25.4 - - + -
142B VAL 3.7 0.3 - - - +
143B CYS* 3.6 0.7 - - - -
144B SER* 2.8 41.6 + - - +
212B VAL* 5.0 3.4 - - - -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 1.3 83.5 - - - +
128B TYR* 1.3 77.4 + - - +
141B LEU* 4.3 4.9 - - + -
142B VAL 3.4 8.3 - - - +
143B CYS* 4.5 4.0 - - - -
157B TRP* 4.1 16.8 - - + -
199B CYS* 4.0 20.4 - - + -
212B VAL* 3.4 40.7 - - + +
213B GLU 5.2 0.4 - - - +
214B TRP* 3.7 34.0 - - + -
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 5.7 7.9 - - + +
182A GLU* 6.0 7.6 - - + -
126B THR* 3.7 21.1 - - + -
127B VAL* 1.3 89.3 - - - +
129B PRO* 1.3 76.1 - - + +
130B THR* 4.1 8.1 - - + -
141B LEU* 4.0 4.0 - - - -
142B VAL* 2.7 65.5 + - + +
144B SER* 4.2 15.4 - - - -
184B LEU* 4.5 10.4 - - - +
214B TRP* 4.8 2.5 - - - -
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 1.3 96.2 - - + +
130B THR* 1.3 74.5 + - - +
139B ASN 6.4 0.2 - - - +
140B LEU 3.5 14.6 - - - +
141B LEU* 4.1 9.2 - - + -
142B VAL* 4.8 0.2 - - - -
191B PRO* 5.7 3.8 - - + -
214B TRP* 4.0 27.8 - - + +
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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