Contacts of the strand formed by residues 135 - 140 (chain B) in PDB entry 5CYO
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 4.6 10.5 - - + -
25B ASN 3.4 3.0 + - - +
26B ILE* 3.4 10.9 - - + +
27B MET 3.0 23.7 + - - -
133B VAL* 3.5 6.7 - - - +
134B HIS* 1.3 83.3 - - - +
136B CYS* 1.3 66.6 + - - +
137B LEU* 4.2 6.5 - - - -
162B VAL* 4.6 0.9 - - - -
163B ASN* 3.6 11.0 - - + -
165B VAL* 3.5 35.2 - - - -
198B TYR* 5.7 0.2 - - - -
265B LEU* 4.1 15.5 - - + -
273B ILE* 4.0 15.5 - - + -
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Residues in contact with CYS 136 (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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27B MET* 3.3 15.7 - - + +
29B VAL* 3.4 39.0 - - - -
133B VAL* 4.9 0.9 - - + -
135B CYS* 1.3 75.9 - - - +
137B LEU* 1.3 66.2 + - - +
138B TYR* 3.4 2.2 + - - -
158B LEU* 4.1 8.1 - - - -
162B VAL* 3.9 12.6 - - + -
163B ASN 2.7 16.0 + - - +
164B ILE* 3.5 22.5 - - + +
165B VAL 2.9 26.9 + - - -
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Residues in contact with LEU 137 (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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26B ILE* 4.0 21.1 - - + -
27B MET 2.7 11.9 + - - +
28B VAL* 3.5 11.5 - - + -
29B VAL 2.9 27.9 + - - +
39B LEU* 4.7 13.9 - - + -
43B LEU* 5.8 6.3 - - + -
135B CYS* 4.4 3.1 - - - -
136B CYS* 1.3 70.2 - - - +
138B TYR* 1.3 61.0 + - - +
139B PHE* 3.5 14.6 - - + -
165B VAL* 3.3 32.8 - - + +
167B VAL* 4.6 5.2 - - + -
261B LEU* 4.2 22.7 - - + -
265B LEU* 3.8 23.6 - - + -
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Residues in contact with TYR 138 (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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29B VAL* 3.5 31.9 - - + -
30B GLY* 4.8 5.5 - - - -
91B PHE* 4.5 2.8 - - - -
136B CYS* 3.4 2.5 + - - +
137B LEU* 1.3 71.7 - - - +
139B PHE* 1.3 71.4 + - - +
140B ILE* 3.6 6.3 + - + +
150B LEU 4.4 0.2 + - - -
151B ASP* 2.5 49.3 + - + -
154B PHE* 3.4 25.5 - + + +
155B MET* 3.4 40.8 - - + -
158B LEU* 3.8 13.7 - - + -
164B ILE* 4.3 16.6 - - + -
165B VAL 3.1 7.5 + - - -
166B PRO* 3.4 5.6 - - + +
167B VAL* 2.8 31.7 + - - +
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Residues in contact with PHE 139 (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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28B VAL* 3.8 25.8 - - + -
29B VAL 2.8 16.8 + - - +
30B GLY* 4.1 4.7 - - - -
34B LEU* 3.5 39.5 - - + +
35B GLY 4.1 6.7 - - - -
36B LYS* 3.6 38.1 - - + -
39B LEU* 3.5 34.5 - - + -
137B LEU* 3.5 21.5 - - + -
138B TYR* 1.3 84.6 - - - +
140B ILE* 1.3 60.9 + - - +
141B PRO* 4.0 2.4 - - - +
151B ASP* 4.7 1.4 - - - +
167B VAL* 3.5 18.8 - - + -
169B ALA* 4.0 9.0 - - + -
170B LYS 6.0 0.2 - - - -
224B VAL* 4.5 4.5 - - + -
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Residues in contact with ILE 140 (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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138B TYR* 4.0 15.5 - - + +
139B PHE* 1.3 75.1 - - - +
141B PRO* 1.3 83.9 - - + +
142B ALA* 3.4 0.5 + - - -
147B LEU* 4.0 32.3 - - + -
151B ASP* 5.0 1.6 - - - +
155B MET* 4.6 4.0 - - - -
166B PRO* 3.8 28.0 - - + -
167B VAL 2.7 18.0 + - - +
168B ILE* 3.7 4.6 - - + +
169B ALA* 2.8 29.0 + - - +
182B PHE* 4.0 19.1 - - + -
186B ILE* 4.0 17.7 - - + -
221B PRO* 4.3 5.8 - - + -
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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