Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 2YYO
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 PHE 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER* 5.9 0.7 - - - -
31A VAL* 3.9 20.0 - - + -
32A ALA 3.8 13.0 - - - +
33A SER 3.6 11.2 - - - -
34A ARG* 3.5 6.1 - - - -
35A PRO* 3.4 42.4 - - + -
60A LEU* 3.3 5.2 - - - -
61A VAL* 2.8 45.9 + - - +
62A PRO 4.0 0.7 - - - -
63A GLN* 3.8 35.2 - - + -
142A ASP 5.2 0.4 - - - -
143A GLY* 3.6 22.4 - - - -
144A LEU* 1.3 74.8 - - - +
146A PRO* 1.3 70.6 - - + +
147A ALA 3.3 0.3 + - - -
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Residues in contact with PRO 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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30A TYR* 4.9 1.5 - - + -
31A VAL* 3.7 0.7 - - - -
32A ALA* 2.9 39.5 + - + +
34A ARG 3.4 20.2 - - - +
36A LEU* 3.6 30.1 - - + +
43A PHE* 3.7 28.9 - - + -
59A GLY 3.6 7.9 - - - +
60A LEU* 3.8 0.9 - - + -
144A LEU 4.0 4.7 - - - +
145A PHE* 1.3 83.9 - - + +
147A ALA* 1.3 59.0 + - - +
159A LEU* 5.4 2.7 - - + -
161A LEU* 4.1 16.6 - - + -
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Residues in contact with ALA 147 (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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29A CYS* 5.2 1.8 - - - -
30A TYR* 3.2 14.4 - - - +
31A VAL* 4.4 3.4 - - + -
43A PHE* 4.1 2.7 - - - -
57A ALA 3.9 0.2 - - - +
58A VAL* 3.6 3.1 - - - +
59A GLY 2.8 33.9 + - - +
61A VAL* 3.7 37.7 - - + -
71A PRO* 4.1 10.0 - - + +
145A PHE 3.9 0.7 - - - +
146A PRO* 1.3 75.3 - - - +
148A VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 148 (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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11A ILE* 4.1 1.6 - - - +
18A LEU* 4.2 23.8 - - + -
29A CYS* 3.5 2.4 - - - -
30A TYR* 2.8 37.6 + - + +
43A PHE* 5.0 0.4 - - + -
45A VAL* 3.9 29.6 - - + -
56A ILE* 4.5 7.0 - - + -
57A ALA 3.2 11.0 - - - +
58A VAL* 4.8 1.1 - - + -
71A PRO* 4.2 4.0 - - - -
147A ALA* 1.3 79.7 - - - +
149A GLY* 1.3 69.8 + - - +
150A MSE 4.4 11.0 - - + -
157A VAL* 4.3 19.5 - - + -
159A LEU* 4.4 10.3 - - + -
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Residues in contact with GLY 149 (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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28A GLY 3.2 7.4 - - - -
29A CYS* 4.4 0.4 - - - -
56A ILE* 3.3 3.8 - - - +
57A ALA 2.8 30.9 + - - +
70A GLN* 2.7 24.9 - - - -
71A PRO* 3.8 8.7 - - - +
148A VAL* 1.3 74.6 - - - +
150A MSE 1.3 69.9 + - - +
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Residues in contact with MSE 150 (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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11A ILE* 3.4 50.0 - - + +
18A LEU* 3.7 26.2 - - + +
20A TYR* 3.7 31.6 - - + +
27A VAL* 3.6 4.9 - - - +
28A GLY 2.7 32.7 + - - +
55A THR 3.6 4.0 - - - -
56A ILE* 4.2 8.5 - - + -
70A GLN* 3.4 1.1 - - - +
148A VAL* 4.4 9.9 - - + -
149A GLY* 1.3 78.6 - - - +
151A HIS* 1.3 62.8 + - - +
155A GLU* 3.1 34.1 - - - +
156A GLU* 4.3 2.0 - - - -
157A VAL* 4.6 9.6 - - - -
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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