Contacts of the strand formed by residues 124 - 130 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F GLU 4.6 3.1 + - - -
123F PRO* 1.3 73.8 - - - +
125F VAL* 1.3 60.3 + - - +
126F THR* 4.0 12.3 + - - +
144F SER* 3.3 4.2 + - - +
145F VAL* 4.6 0.2 - - - -
146F SER* 3.0 44.7 + - - +
147F ASP* 4.7 6.5 - - - +
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Residues in contact with VAL 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO* 3.8 10.9 + - + +
124F THR* 1.3 76.1 - - - +
126F THR* 1.3 70.4 + - - +
143F CYS* 3.8 27.8 - - - -
144F SER 3.3 4.5 - - - +
145F VAL* 4.5 9.9 - - + -
199F CYS* 4.7 3.1 - - + +
201F VAL* 3.9 28.3 - - + -
210F VAL* 4.1 20.6 - - + -
212F VAL* 3.7 34.3 - - + +
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E PRO* 5.6 9.0 - - + +
124F THR* 4.7 11.1 + - - +
125F VAL* 1.3 76.8 + - - +
127F VAL* 1.3 77.2 + - - +
128F TYR* 4.2 13.9 - - + -
142F VAL 3.7 0.3 - - - +
143F CYS* 3.7 0.5 - - - -
144F SER* 2.8 43.1 + - - -
212F VAL* 5.0 2.5 - - - -
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Residues in contact with VAL 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F THR* 1.3 87.7 - - - +
128F TYR* 1.3 71.4 + - - +
141F LEU* 4.2 4.9 - - + -
142F VAL 3.3 4.7 - - - +
143F CYS* 4.5 2.2 - - - -
157F TRP* 3.6 26.5 - - + -
199F CYS* 3.9 22.4 - - + -
212F VAL* 3.5 38.9 - - + +
213F GLU 5.2 0.2 - - - +
214F TRP* 3.7 37.4 - - + -
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Residues in contact with TYR 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PRO* 5.7 8.0 - - + +
126F THR* 4.2 13.0 - - + -
127F VAL* 1.3 83.2 - - - +
129F PRO* 1.3 77.0 - - + +
130F THR* 3.6 17.7 - - + -
141F LEU* 3.9 4.0 - - - -
142F VAL* 2.6 74.2 + - + +
144F SER* 4.0 16.9 - - - -
184F LEU* 4.1 14.2 - - - +
214F TRP* 4.6 2.5 - - - +
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Residues in contact with PRO 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F TYR* 1.3 94.5 - - + +
130F THR* 1.3 69.8 + - - +
139F ASN* 5.4 6.1 - - - +
140F LEU 3.2 11.2 - - - +
141F LEU* 4.0 12.8 - - + -
191F PRO* 5.2 6.3 - - + -
214F TRP* 3.9 31.4 - - + +
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Residues in contact with THR 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E GLU 5.7 4.9 - - - +
128F TYR* 3.6 24.9 - - + -
129F PRO* 1.3 80.7 - - - +
131F LYS* 1.3 78.6 + - - +
132F THR* 4.0 1.8 - - - -
139F ASN* 3.8 5.6 + - - -
140F LEU* 3.0 40.4 + - - +
142F VAL* 3.7 14.6 - - + +
186F MET* 5.2 1.9 - - + +
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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