Contacts of the helix formed by residues 156 - 163 (chain B) in PDB entry 1YF9
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 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 4.1 1.3 - - - -
152B SER* 3.6 23.6 - - - +
153B THR 4.2 9.2 - - - +
154B HIS 3.5 1.4 - - - -
155B ALA* 1.3 80.2 - - - +
157B PRO* 1.3 74.1 - - + +
158B GLN* 3.6 11.0 + - - +
159B LYS* 2.9 28.8 + - + +
160B ALA* 3.0 22.3 + - - +
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Residues in contact with PRO 157 (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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43B GLU* 6.0 1.1 - - - +
45B LYS* 5.2 5.2 - - - +
54B ASP 5.8 2.2 - - - +
56B THR* 3.9 29.3 - - + +
155B ALA 4.4 0.4 - - - +
156B THR* 1.3 86.6 - - + +
158B GLN* 1.3 57.9 + - + +
160B ALA* 3.5 2.3 + - - +
161B LEU* 3.1 29.5 + - - +
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Residues in contact with GLN 158 (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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156B THR* 3.1 9.8 + - - +
157B PRO* 1.3 78.7 - - + +
159B LYS* 1.3 68.8 + - - +
161B LEU* 3.3 8.9 + - + +
162B GLU* 3.0 46.1 + - + +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 3.9 6.7 - - + +
153B THR* 3.3 29.4 - - - +
154B HIS* 3.4 32.8 - - + +
156B THR* 2.9 21.4 + - + +
158B GLN* 1.3 81.9 - - - +
160B ALA* 1.3 61.0 + - - +
162B GLU* 3.6 25.0 + - - +
163B SER* 3.3 23.6 + - - -
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Residues in contact with ALA 160 (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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56B THR* 3.7 26.5 - - + +
57B TRP* 3.8 20.0 - - - -
58B MET* 3.4 19.4 - - + +
78B ASN* 3.9 6.8 - - - +
156B THR 3.0 15.9 + - - +
157B PRO 3.7 5.2 - - - +
159B LYS* 1.3 77.0 - - - +
161B LEU* 1.3 60.9 + - - +
163B SER* 2.7 25.6 + - - -
164B ILE 3.9 0.2 + - - -
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Residues in contact with LEU 161 (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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32B TYR* 3.8 29.6 - - + +
43B GLU* 5.8 1.3 - - - +
58B MET* 4.3 6.2 - - + +
157B PRO 3.1 17.6 + - - +
158B GLN* 3.3 7.2 + - + +
160B ALA* 1.3 77.4 - - - +
162B GLU* 1.3 60.4 + - - +
163B SER 3.3 1.0 + - - -
164B ILE* 3.4 22.1 + - + +
169B ARG* 3.5 18.0 - - + +
170B PRO* 4.2 25.6 - - + +
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Residues in contact with GLU 162 (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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158B GLN* 3.0 36.9 + - - +
159B LYS* 3.6 35.3 + - + +
161B LEU* 1.3 76.0 - - - +
163B SER* 1.3 56.3 + - - +
164B ILE 3.2 2.0 - - - -
169B ARG* 3.1 38.6 + - - +
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Residues in contact with SER 163 (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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58B MET* 3.4 6.6 - - - +
77B CYS* 3.3 38.1 - - - +
78B ASN* 3.7 15.0 + - - -
159B LYS 3.3 12.7 + - - -
160B ALA* 2.7 20.8 + - - -
161B LEU 3.2 0.4 - - - -
162B GLU* 1.3 75.4 - - - +
164B ILE* 1.3 63.3 + - - +
165B PRO* 3.6 6.8 - - - +
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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