Contacts of the helix formed by residues 138 - 146 (chain A) in PDB entry 1YYH
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 GLY 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A GLN* 5.3 2.2 - - - -
136A VAL 3.6 2.4 + - - -
137A GLU* 1.3 74.8 - - - +
139A MET* 1.3 62.5 + - - +
140A LEU* 3.4 2.7 - - - -
141A GLU* 3.3 10.9 + - - +
142A ASP* 3.0 31.3 + - - +
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.6 17.7 - - - +
98A VAL* 3.7 26.2 - - + -
101A ASP* 3.6 20.2 - - - +
102A ALA 3.8 8.5 - - - +
103A GLN* 3.8 15.5 - - - +
106A PHE* 3.5 53.3 - - + -
131A ALA* 4.4 11.2 - - + -
136A VAL* 3.8 15.1 + - + -
137A GLU 3.0 14.4 + - - +
138A GLY* 1.3 73.8 - - - +
140A LEU* 1.3 68.4 + - - +
142A ASP 3.2 0.9 + - - -
143A LEU* 2.9 30.1 + - + +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.6 30.7 - - + +
131A ALA* 3.9 16.9 - - + +
132A ALA* 3.8 32.8 - - + +
136A VAL 5.1 5.6 + - - +
138A GLY 3.4 0.4 - - - -
139A MET* 1.3 79.0 - - - +
141A GLU* 1.3 61.9 + - + +
143A LEU* 3.3 2.5 + - - +
144A ILE* 3.1 39.0 + - + +
172A ALA* 3.9 26.2 - - + +
175A VAL* 3.8 24.0 - - + -
176A LEU* 4.2 8.7 - - + -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY* 3.3 11.3 + - - +
139A MET 3.3 0.6 - - - -
140A LEU* 1.3 79.3 - - + +
142A ASP* 1.3 59.0 + - - +
144A ILE* 3.4 3.5 + - + +
145A ASN* 2.9 48.2 + - - +
175A VAL* 4.0 40.0 - - + +
178A LYS* 6.1 0.7 - - - +
179A ASN* 5.2 4.2 + - - +
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Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLN* 5.0 1.9 - - - +
106A PHE* 3.6 16.4 - - + -
107A GLN* 2.7 29.9 + - - -
110A ILE* 3.9 9.2 - - + -
138A GLY* 3.0 21.1 + - - +
139A MET 3.6 7.0 - - - +
141A GLU* 1.3 75.5 - - - +
143A LEU* 1.3 60.5 + - - +
145A ASN* 3.3 12.4 + - - +
146A SER* 3.0 32.9 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.3 10.8 - - + -
98A VAL* 4.9 1.3 - - + -
106A PHE* 3.9 14.1 - - + -
110A ILE* 3.9 25.6 - - + -
117A LEU* 4.3 20.6 - - + +
127A PRO* 3.7 14.1 - - + +
128A LEU* 3.7 41.1 - - + +
131A ALA* 4.5 4.3 - - + -
139A MET 2.9 25.9 + - - +
140A LEU 3.6 4.0 - - - +
142A ASP* 1.3 72.6 - - - +
144A ILE* 1.3 63.9 + - - +
146A SER* 3.2 7.2 + - - -
147A HIS 3.2 5.7 + - - -
148A ALA* 3.0 28.9 + - + +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.7 18.2 - - + -
140A LEU* 3.1 23.5 + - + +
141A GLU* 3.7 4.0 - - + +
143A LEU* 1.3 78.3 - - - +
145A ASN* 1.3 63.3 + - - +
147A HIS* 2.9 24.3 + - - -
148A ALA 4.5 9.5 - - - +
150A VAL* 5.0 8.5 - - + -
175A VAL* 3.8 24.0 - - + +
176A LEU* 3.8 29.6 - - + -
179A ASN* 3.4 38.4 - - + +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 2.9 42.8 + - - +
142A ASP* 3.7 12.0 + - - +
143A LEU 3.3 0.4 - - - -
144A ILE* 1.3 81.9 - - - +
146A SER* 1.3 57.4 + - - +
147A HIS* 3.4 21.9 + - - -
179A ASN* 4.8 5.5 + - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.8 27.6 + - - +
117A LEU* 3.2 27.7 - - - +
142A ASP 3.0 17.4 + - - -
143A LEU* 3.2 4.9 + - - -
144A ILE 3.2 0.2 - - - -
145A ASN* 1.3 73.7 - - - +
147A HIS* 1.3 72.3 + - - +
148A ALA 3.5 0.4 - - - -
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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