Contacts of the strand formed by residues 135 - 141 (chain C) in PDB entry 5CYP
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 CYS 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.2 12.3 - - + -
25C ASN 3.1 8.4 + - - +
26C ILE* 3.3 10.7 - - + -
27C MET 2.8 23.6 + - - -
133C VAL* 3.4 7.2 - - - +
134C HIS* 1.3 79.0 - - - +
136C CYS* 1.3 65.6 + - - +
137C LEU* 4.2 6.1 - - - -
163C ASN* 3.6 5.8 - - - -
165C VAL* 4.1 16.6 - - - -
265C LEU* 3.7 37.5 - - - -
273C ILE* 4.1 14.6 - - + -
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Residues in contact with CYS 136 (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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27C MET* 3.2 19.3 - - - +
29C VAL* 3.7 27.8 - - - -
133C VAL* 4.5 5.4 - - + -
135C CYS* 1.3 77.2 - - - +
137C LEU* 1.3 70.2 + - - +
138C TYR* 3.5 1.5 + - - -
158C LEU* 4.2 17.9 - - - -
162C VAL* 3.9 19.5 - - + -
163C ASN 2.7 14.7 + - - +
164C ILE* 3.2 8.9 - - + +
165C VAL 2.9 23.7 + - - -
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Residues in contact with LEU 137 (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 ILE* 4.2 16.6 - - + -
27C MET 2.8 10.8 + - - +
28C VAL* 4.4 10.8 - - + -
29C VAL* 2.8 31.9 + - - +
39C LEU* 4.0 26.9 - - + -
43C LEU* 5.5 7.6 - - + -
135C CYS* 4.2 2.6 - - - -
136C CYS* 1.3 72.2 - - - +
138C TYR* 1.3 59.8 + - - +
139C PHE* 4.1 13.6 - - + -
165C VAL* 3.4 28.3 - - + +
167C VAL* 4.4 5.6 - - + -
258C PHE* 5.8 0.7 - - + -
261C LEU* 4.3 17.7 - - + -
265C LEU* 3.8 26.5 - - + -
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Residues in contact with TYR 138 (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 VAL* 3.3 16.8 - - + -
91C PHE* 3.3 12.3 - + - -
136C CYS 3.5 4.6 + - - +
137C LEU* 1.3 72.0 - - - +
139C PHE* 1.3 73.9 + - - +
140C ILE* 3.6 6.0 + - + +
151C ASP* 2.8 37.9 + - + -
154C PHE* 3.2 41.5 - + + +
155C MET* 3.6 42.6 - - + -
158C LEU* 3.7 17.9 - - + -
164C ILE* 5.0 6.3 - - + -
165C VAL 3.1 8.2 + - - +
166C PRO* 3.3 11.3 - - + +
167C VAL* 2.7 34.1 + - - +
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Residues in contact with PHE 139 (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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28C VAL* 3.9 21.1 - - + -
29C VAL 2.7 22.8 + - - +
30C GLY* 4.0 7.3 - - - -
31C GLN 4.4 0.7 + - - -
34C LEU* 3.4 33.0 - - + +
35C GLY 3.9 16.6 - - - -
36C LYS* 3.5 28.7 - - + -
39C LEU* 3.5 30.3 - - + -
137C LEU* 4.1 12.6 - - + -
138C TYR* 1.3 86.1 - - - +
140C ILE* 1.3 61.2 + - - +
141C PRO* 3.7 3.3 - - - +
151C ASP* 5.0 0.9 - - - +
167C VAL* 3.6 14.8 - - + -
169C ALA* 3.6 20.4 - - + -
224C VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 140 (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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138C TYR* 4.2 17.5 - - + +
139C PHE* 1.3 75.6 - - - +
141C PRO* 1.3 81.6 - - + +
142C ALA 3.5 0.7 + - - -
147C LEU* 3.7 27.8 - - + -
151C ASP* 4.9 1.8 - - - +
155C MET* 4.6 7.2 - - - -
166C PRO* 4.0 19.3 - - + -
167C VAL 2.7 18.0 + - - +
168C ILE* 3.7 4.4 - - - +
169C ALA* 2.9 24.4 + - - -
182C PHE* 3.9 16.2 - - + -
186C ILE* 3.7 33.9 - - + -
221C PRO* 4.5 3.6 - - + -
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Residues in contact with PRO 141 (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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31C GLN* 4.7 4.7 - - + +
34C LEU* 3.8 31.6 - - + -
139C PHE 3.7 6.5 - - - +
140C ILE* 1.3 88.4 - - + +
142C ALA* 1.3 52.7 + - - +
143C THR* 2.7 31.3 + - + +
148C ARG* 3.3 34.8 - - - +
151C ASP* 3.6 16.4 - - - +
169C ALA* 4.7 0.7 - - + -
182C PHE* 3.5 11.3 - - - -
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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