Contacts of the helix formed by residues 120 - 126 (chain B) in PDB entry 1YI8
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 1.3 80.8 - - - +
121B VAL* 1.3 64.1 + - - +
122B SER* 3.5 7.0 + - - -
123B HIS* 3.0 32.4 + - + +
124B LEU* 3.1 17.6 + - - +
142C ARG* 3.8 50.2 + - + +
143C VAL 3.0 12.3 - - - +
144C PRO* 4.8 2.5 - - + -
145C ALA 4.4 0.4 - - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 1.3 71.7 - - - +
122B SER* 1.3 57.3 + - - +
124B LEU* 3.3 10.3 + - - +
125B ARG* 2.9 41.6 + - - +
148B PHE* 3.6 19.8 - - + -
121C VAL* 5.5 1.6 - - + -
141C GLU 4.4 5.1 + - - +
143C VAL* 2.7 22.5 + - + +
145C ALA* 4.1 10.1 - - + -
148C PHE* 3.5 52.5 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.1 6.4 + - - -
121B VAL* 1.3 77.6 - - - +
123B HIS* 1.3 63.0 + - - +
125B ARG* 3.5 16.2 + - - +
126B GLN* 3.5 18.8 + - - +
141C GLU* 2.8 52.3 + - - +
142C ARG* 5.1 3.1 - - - -
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.7 12.8 - - + +
120B THR* 3.0 23.6 + - + +
122B SER* 1.3 76.2 - - - +
124B LEU* 1.3 65.6 + - - +
126B GLN* 3.1 41.3 + - + +
127B ASN* 3.9 4.3 + - - +
178B GLN* 2.9 39.5 + - + -
181B GLU* 5.6 11.1 + - + +
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Residues in contact with LEU 124 (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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119B VAL* 4.1 7.2 - - + -
120B THR 3.1 12.1 + - - +
121B VAL* 3.6 5.2 - - + +
123B HIS* 1.3 76.5 - - - +
125B ARG* 1.3 61.9 + - - +
126B GLN 3.3 0.3 + - - -
127B ASN* 3.4 19.0 + - + +
130B VAL* 3.9 8.8 - - - +
148B PHE* 3.4 48.4 - - + +
149B VAL* 4.4 12.3 - - + -
151B PRO* 5.1 5.4 - - + -
152B VAL* 3.7 25.6 - - + -
178B GLN* 3.8 22.2 - - - +
145C ALA* 3.9 27.6 - - + -
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Residues in contact with ARG 125 (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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121B VAL* 2.9 26.4 + - - +
122B SER* 3.6 13.0 - - - +
123B HIS 3.1 0.4 - - - -
124B LEU* 1.3 79.5 - - - +
126B GLN* 1.3 57.4 + - - +
127B ASN 3.4 2.3 + - - +
130B VAL* 5.5 0.6 - - - +
131B LYS* 4.4 20.2 - - - +
141B GLU* 3.1 29.3 + - - +
143B VAL* 6.1 3.2 - - - +
148B PHE* 3.8 23.9 - - + -
121C VAL* 3.7 19.2 - - - +
125C ARG* 5.6 9.5 - - - +
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Residues in contact with GLN 126 (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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122B SER 3.6 9.0 + - - +
123B HIS* 3.1 46.5 - - + +
125B ARG* 1.3 78.2 - - - +
127B ASN* 1.3 62.7 + - - +
128B PRO* 3.2 10.6 - - - +
131B LYS* 5.7 2.7 - - - -
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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