Contacts of the strand formed by residues 55 - 60 (chain C) in PDB entry 1YI8
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 GLU 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.8 18.4 - - + +
22C ARG 4.8 3.9 - - - +
23C PRO 3.2 10.2 + - - +
24C ARG* 2.9 44.3 + - - +
25C VAL* 2.9 26.0 + - - +
54C ALA* 1.3 73.4 - - - +
56C LEU* 1.3 61.6 + - - +
57C PHE* 3.4 10.0 + - + -
96C LYS 5.4 4.5 - - - +
98C THR* 5.3 1.6 - - - +
330C ARG* 2.6 33.6 + - - -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.7 27.8 - - + +
27C THR* 3.9 12.8 - - + +
47C ARG* 4.6 17.7 - - + +
50C LEU* 4.7 9.6 - - + +
51C GLN* 4.1 23.5 - - + +
54C ALA 3.6 2.2 + - - -
55C GLU* 1.3 73.7 - - - +
57C PHE* 1.3 76.7 + - - +
58C VAL* 3.1 31.6 - - + -
92C LEU* 5.0 3.6 - - + -
96C LYS 4.3 6.3 + - - +
97C THR* 3.6 20.6 - - + -
98C THR* 3.0 25.5 + - - -
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 3.4 38.8 - - + -
25C VAL 2.9 11.9 + - - +
26C LEU* 3.6 16.2 - - + -
27C THR* 3.0 29.6 + - - -
55C GLU* 3.4 21.5 - - + -
56C LEU* 1.3 82.3 - - - +
58C VAL* 1.3 62.7 + - - +
98C THR* 3.3 37.2 - - + +
100C VAL* 4.7 7.0 - - + -
161C PHE* 4.2 31.6 - + + -
330C ARG* 4.0 11.2 - - + -
331C GLY* 4.6 4.3 - - - -
334C VAL* 4.3 15.5 - - + -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 5.1 0.7 - - - -
27C THR* 3.3 17.9 - - - +
47C ARG* 4.5 7.9 - - - +
56C LEU* 3.1 25.8 - - + -
57C PHE* 1.3 73.4 - - - +
59C LEU* 1.3 61.1 + - - +
60C LEU 3.9 0.3 + - - -
87C TYR* 3.6 28.3 - - + +
92C LEU* 4.0 17.3 - - + -
97C THR* 4.1 4.9 - - - +
98C THR 2.9 10.2 + - - +
99C CYS* 3.3 28.7 - - + -
100C VAL* 2.8 29.6 + - - +
323C PHE* 5.1 0.2 - - + -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.7 10.3 - - + +
27C THR 2.8 15.2 + - - +
28C GLY* 3.2 2.9 - - - -
29C ASP 3.0 26.3 + - - -
58C VAL* 1.3 73.3 - - - +
60C LEU* 1.3 60.4 + - - +
61C ALA* 3.2 12.8 + - + +
87C TYR* 3.8 1.7 + - - -
100C VAL* 3.4 33.7 - - + +
102C GLN* 3.7 30.5 - - + +
108C LEU* 4.5 0.7 - - + -
157C ASP* 3.6 37.0 - - + +
161C PHE* 4.1 11.7 - - + -
3000C TRP* 3.9 16.8 - - + +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP 3.7 4.5 - - - +
31C PRO* 3.9 11.2 - - + -
59C LEU* 1.3 70.2 - - - +
61C ALA* 1.3 59.3 + - - +
62C ASP* 2.9 12.2 + - - +
80C VAL* 3.6 35.0 - - + +
83C VAL* 3.2 27.4 - - + -
84C ALA* 4.3 2.0 - - + +
87C TYR* 3.4 31.4 - - + +
99C CYS* 3.5 27.8 - - - -
100C VAL 2.7 13.5 + - - +
101C VAL* 3.8 9.5 - - + -
102C GLN 3.1 17.7 + - - -
324C VAL* 4.0 11.4 - - + -
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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