Contacts of the helix formed by residues 138 - 146 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLN* 4.9 2.7 - - - -
136B VAL 3.5 3.2 + - - -
137B GLU* 1.3 71.0 + - - +
139B MET* 1.3 63.2 + - - +
140B LEU 3.3 2.6 + - - -
141B GLU* 3.4 10.8 + - - +
142B ASP* 3.1 31.8 + - - +
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Residues in contact with MET 139 (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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97B ALA 3.7 15.5 - - - +
98B VAL* 3.8 25.4 - - + -
101B ASP* 3.7 12.1 - - - +
102B ALA 3.8 11.2 - - - +
103B GLN* 3.4 27.6 - - - +
106B PHE* 3.5 55.9 - - + -
131B ALA* 4.5 11.2 - - + -
136B VAL* 3.7 16.5 + - + -
137B GLU 2.8 11.0 + - - +
138B GLY* 1.3 72.9 - - - +
140B LEU* 1.3 58.8 + - - +
142B ASP 3.3 0.3 + - - -
143B LEU* 2.8 35.6 + - + +
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Residues in contact with LEU 140 (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 LEU* 3.6 31.8 - - + +
131B ALA* 4.0 18.7 - - + +
132B ALA* 3.8 30.7 - - + +
136B VAL 5.2 4.7 + - - +
138B GLY 3.3 1.2 - - - +
139B MET* 1.3 79.1 - - - +
141B GLU* 1.3 64.2 + - - +
143B LEU* 4.7 0.2 - - - -
144B ILE* 3.1 42.3 + - + +
172B ALA* 3.8 27.8 - - + +
175B VAL* 3.8 21.3 - - + -
176B LEU* 4.2 9.6 - - + -
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Residues in contact with GLU 141 (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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138B GLY* 3.4 11.1 + - - +
139B MET 3.3 0.4 - - - -
140B LEU* 1.3 81.4 - - - +
142B ASP* 1.3 53.7 + - - +
144B ILE* 3.3 2.5 + - - +
145B ASN* 2.8 52.1 + - - +
175B VAL* 3.9 39.9 - - + +
179B ASN* 5.7 1.3 + - - +
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Residues in contact with ASP 142 (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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103B GLN* 4.8 2.3 - - - +
106B PHE* 3.6 20.0 - - + -
107B GLN* 2.8 28.9 + - - -
110B ILE* 3.9 9.1 - - + +
138B GLY* 3.1 24.8 + - - +
139B MET 3.7 0.2 - - - +
141B GLU* 1.3 76.7 - - - +
143B LEU* 1.4 63.9 + - - +
145B ASN* 3.3 13.0 + - - +
146B SER* 3.0 27.2 + - - -
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Residues in contact with LEU 143 (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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94B LEU* 4.1 16.2 - - + -
98B VAL* 4.8 1.1 - - + -
106B PHE* 3.9 14.6 - - + -
110B ILE* 3.9 24.9 - - + -
117B LEU* 4.3 16.7 - - + +
127B PRO* 3.7 15.9 - - + +
128B LEU* 3.7 42.2 - - + +
131B ALA* 4.5 4.3 - - + -
139B MET 2.8 27.1 + - - +
140B LEU 3.6 3.6 - - - +
142B ASP* 1.4 71.4 - - - +
144B ILE* 1.3 63.9 + - - +
146B SER* 3.1 13.0 + - - -
147B HIS 3.2 0.7 + - - -
148B ALA* 3.0 27.2 + - + +
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Residues in contact with ILE 144 (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 LEU* 3.7 13.0 - - + -
140B LEU* 3.1 28.9 + - + +
141B GLU* 3.6 6.7 - - - +
143B LEU* 1.3 76.1 - - - +
145B ASN* 1.3 66.1 + - - +
147B HIS* 3.0 18.4 + - - -
148B ALA 4.4 7.6 - - - +
150B VAL* 4.0 17.5 - - + -
175B VAL* 3.6 24.5 - - + +
176B LEU* 3.8 23.8 - - + -
179B ASN* 3.3 39.0 - - + +
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Residues in contact with ASN 145 (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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141B GLU* 2.8 45.2 + - - +
142B ASP* 3.8 13.2 + - - +
144B ILE* 1.3 78.4 - - - +
146B SER* 1.3 59.4 + - - +
147B HIS* 3.2 20.4 + - - -
179B ASN* 4.8 6.1 + - - +
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Residues in contact with SER 146 (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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110B ILE* 3.8 26.5 + - - +
117B LEU* 3.1 28.8 - - - +
142B ASP 3.0 17.2 + - - -
143B LEU* 3.1 4.0 + - - -
145B ASN* 1.3 73.6 - - - +
147B HIS* 1.3 72.5 + - - +
148B ALA 3.5 1.8 - - - -
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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