Contacts of the helix formed by residues 135 - 141 (chain B) in PDB entry 5SY1
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 TYR 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A TYR* 4.2 7.6 + - - +
93B VAL* 4.4 16.2 - - + +
96B VAL* 3.7 32.7 - - + +
97B LEU* 4.0 16.6 - - + -
100B LYS* 5.6 1.1 - - + -
131B TYR* 3.0 50.8 + + - +
132B PRO 4.1 1.1 - - - -
134B LEU* 1.3 94.2 - - + +
136B TYR* 1.3 63.7 + - - +
137B PRO* 3.5 1.8 - - - -
138B LEU* 3.3 43.4 + - + +
139B LEU 4.0 2.3 + - - -
160B HIS* 4.1 25.0 - + + +
189B GLN* 4.1 12.5 + - - -
193B LEU* 4.8 8.8 - - + +
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 4.0 10.8 - - + -
494A TYR* 4.1 22.9 - + - -
52B MET* 3.5 44.2 - - + -
55B LEU* 5.9 0.9 - - + -
74B LEU* 3.7 18.9 - - + +
75B LEU* 2.4 39.2 + - + +
76B SER 4.3 0.7 - - - -
77B PRO* 4.0 26.2 - - + -
132B PRO 3.3 18.0 + - - +
133B THR* 3.4 13.0 - - - +
134B LEU 3.2 2.8 - - - -
135B TYR* 1.3 77.6 - - - +
137B PRO* 1.3 60.7 - - + +
138B LEU 3.2 0.9 + - - -
139B LEU* 3.4 5.5 + - + +
140B ALA* 3.2 29.8 + - + +
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.7 19.5 - - - +
51B VAL* 3.9 26.9 - - + +
52B MET* 3.7 23.3 - - + +
55B LEU* 5.3 1.1 - - + +
133B THR 4.2 3.4 - - - +
134B LEU 3.6 14.1 - - - +
135B TYR 3.8 0.7 - - - -
136B TYR* 1.3 92.1 - - + +
138B LEU* 1.3 62.0 + - + +
140B ALA* 3.5 13.7 + - + +
141B CYS* 3.3 24.9 + - - -
156B LEU* 4.2 11.5 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.4 13.0 - - + -
135B TYR* 3.4 43.7 - - + +
136B TYR 3.1 1.2 - - - -
137B PRO* 1.3 81.1 - - + +
139B LEU* 1.3 59.8 + - - +
141B CYS* 3.7 4.2 + - - +
153B GLY* 4.3 7.6 - - - +
156B LEU* 3.8 30.3 - - + -
157B SER* 4.2 14.8 - - - +
160B HIS* 4.7 12.6 - - + +
193B LEU* 5.2 2.9 - - + -
196B LEU* 4.2 19.7 - - + -
200B TYR* 2.2 41.8 + - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TYR* 3.7 39.7 - - + +
77B PRO* 4.3 19.7 - - + -
78B VAL* 3.5 30.7 + - + +
80B PHE* 6.0 2.0 - - + -
89B LEU* 3.9 13.6 - - + +
90B ALA* 3.8 24.7 - - + +
93B VAL* 3.7 32.3 - - + -
94B TYR* 5.0 8.3 - - + -
135B TYR 4.0 1.2 + - - +
136B TYR* 3.4 7.1 + - + +
138B LEU* 1.3 79.4 - - - +
140B ALA* 1.3 62.2 + - - +
141B CYS 3.2 0.7 + - - -
142B GLY* 3.4 9.9 + - - -
143B THR* 4.4 1.2 + - - +
200B TYR* 4.3 1.1 - - - -
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Residues in contact with ALA 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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55B LEU* 3.7 24.4 - - + +
75B LEU* 4.1 13.1 - - + +
76B SER 5.0 1.1 - - - +
77B PRO* 4.9 7.9 - - - -
136B TYR* 3.2 35.7 + - + +
137B PRO* 3.9 8.1 - - + +
138B LEU 3.2 1.6 - - - -
139B LEU* 1.3 77.8 - - - +
141B CYS* 1.3 57.9 + - - +
142B GLY 3.3 0.2 - - - -
143B THR* 3.0 24.4 + - - -
144B LEU* 4.8 2.4 - - - +
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Residues in contact with CYS 141 (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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51B VAL* 5.3 7.2 - - - -
55B LEU* 5.3 8.1 - - - -
137B PRO 3.3 17.7 + - - -
138B LEU 4.1 7.2 - - - +
139B LEU 3.2 1.2 - - - -
140B ALA* 1.3 78.9 - - - +
142B GLY* 1.3 62.5 + - - +
143B THR 3.1 1.2 + - - -
144B LEU* 3.4 17.5 + - - +
145B HIS 4.2 4.0 + - - -
149B GLY* 3.3 40.1 - - - +
150B TYR* 5.0 7.3 - - + -
152B LEU* 4.4 7.4 - - - -
153B GLY* 3.6 21.5 - - - -
156B LEU* 5.4 0.9 - - - -
200B TYR* 4.6 7.6 - - + +
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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