Contacts of the strand formed by residues 27 - 31 (chain E) in PDB entry 1YRY
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 VAL 27 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E PRO* 4.2 0.3 - - - +
26E GLN* 1.3 83.5 - - - +
28E ALA* 1.3 62.4 + - - +
29E ILE* 4.0 7.9 - - + -
76E ARG* 3.6 21.8 - - + -
77E ALA 3.2 2.8 + - - +
78E CYS* 3.2 15.6 - - - +
79E VAL* 3.1 26.5 + - - +
108E VAL* 4.5 0.4 - - - -
110E THR* 3.6 9.4 - - - +
112E VAL* 3.5 30.7 - - + -
279E MET* 4.1 3.6 - - - -
282E ILE* 3.5 42.0 - - + -
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Residues in contact with ALA 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 1.3 71.9 - - - +
29E ILE* 1.3 61.0 + - - +
79E VAL* 3.3 12.8 - - + -
103E PHE* 3.2 35.2 - - + -
108E VAL* 3.5 19.5 - - + +
110E THR 2.8 8.8 + - - +
111E LEU* 3.1 10.6 - - + +
112E VAL* 2.9 25.5 + - - +
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Residues in contact with ILE 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 4.0 5.2 - - + -
28E ALA* 1.3 73.7 - - - +
30E ILE* 1.3 73.5 + - - +
31E CYS 3.9 0.2 - - - -
38E LEU* 3.8 24.0 - - + -
73E LEU* 4.1 5.2 - - + -
78E CYS* 3.9 17.3 - - - -
79E VAL 2.9 8.9 + - - +
80E MET* 3.4 33.4 - - + +
81E MET* 2.8 27.9 + - - +
103E PHE* 5.1 0.3 - - - -
112E VAL* 3.3 34.5 - - + +
114E THR* 5.1 1.8 - - + -
275E VAL* 4.0 10.1 - - + -
279E MET* 3.9 17.5 - - + -
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Residues in contact with ILE 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 1.3 80.7 - - - +
31E CYS* 1.3 54.3 + - - +
81E MET* 3.5 38.8 - - + +
84E ARG* 3.2 41.7 - - + +
100E VAL* 4.1 5.2 - - + -
103E PHE* 4.0 12.8 - - + -
111E LEU* 3.5 26.7 - - + -
112E VAL 3.0 10.8 + - - +
113E VAL* 4.6 4.0 - - + -
114E THR* 2.8 38.6 + - - +
224E GLU* 4.0 22.4 - - + +
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Residues in contact with CYS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 4.6 0.4 - - - -
30E ILE* 1.3 74.4 - - - +
32E GLY* 1.3 62.5 + - - +
35E LEU 3.1 30.5 - - - +
36E GLY* 3.9 11.9 - - - -
38E LEU* 3.8 17.5 - - - -
39E THR* 5.0 0.7 - - - -
80E MET* 3.6 30.5 - - - -
81E MET 3.1 17.5 + - - +
82E GLN* 4.7 4.3 - - - -
83E GLY* 4.1 4.4 + - - +
84E ARG* 4.1 18.4 + - - +
114E THR* 3.2 7.4 - - - -
292E SO4 5.2 0.2 - - - +
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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