Contacts of the strand formed by residues 145 - 151 (chain H) in PDB entry 5DSV
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 GLY 145 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40H ARG* 6.0 0.4 - - - -
139H SER* 3.9 1.4 + - - +
140H TYR* 3.5 13.3 - - - -
141H SER 2.9 33.3 + - - +
142H VAL 3.6 6.1 + - - -
143H ASN 3.5 2.2 - - - -
144H ASP* 1.3 84.8 - - - +
146H ALA* 1.3 61.3 + - - -
147H GLN* 4.0 3.8 + - - +
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Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ARG* 3.1 41.4 + - + +
41H CYS 4.3 2.7 - - - +
42H LYS 4.7 4.9 + - - +
44H GLY* 3.4 42.4 - - - +
139H SER 3.6 5.8 - - - -
140H TYR* 3.5 8.7 - - + -
144H ASP 4.5 1.4 - - - +
145H GLY* 1.3 70.1 - - - -
147H GLN* 1.3 69.0 + - - +
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Residues in contact with GLN 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ARG* 4.4 5.2 - - - +
45H VAL* 3.5 7.2 - - - +
107H PRO* 5.0 0.4 - - - +
108H LEU* 3.4 36.3 - - + +
109H LYS* 3.6 36.0 - - - +
138H GLY* 3.3 4.2 - - - -
139H SER* 3.0 38.5 + - - +
144H ASP* 3.8 34.2 + - - +
145H GLY 4.0 8.5 - - - +
146H ALA* 1.3 82.2 - - - +
148H LEU* 1.3 60.6 + - - +
149H TYR* 4.0 9.5 + - + -
59I GLU* 5.5 2.8 - - - +
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Residues in contact with LEU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLY 3.7 10.1 - - - +
39H ILE* 3.9 5.8 - - - +
40H ARG* 4.6 7.4 - - + +
45H VAL* 3.9 13.9 - - + -
47H PHE* 3.5 38.6 - - + -
136H MET* 4.2 13.2 - - + -
137H LEU 3.4 6.7 - - - +
147H GLN* 1.3 75.9 - - - +
149H TYR* 1.3 67.5 + - - +
159H GLY* 3.5 4.7 - - - -
160H TYR* 2.9 55.7 + - + +
161H TRP 4.0 2.5 - - - +
162H GLY* 3.7 30.3 - - - -
163H CYS 4.1 2.5 - - - +
59I GLU* 5.6 0.2 - - - +
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Residues in contact with TYR 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H LEU* 3.7 20.4 - - + -
109H LYS* 3.4 47.3 - - - +
112H ALA* 3.9 18.8 - - + -
136H MET* 2.9 9.4 - - - +
137H LEU* 2.8 44.3 + - + +
147H GLN* 4.0 16.1 + - + -
148H LEU* 1.3 81.2 - - - +
150H MET* 1.3 60.2 + - - +
151H ILE* 5.1 1.8 - - + -
157H SER* 3.6 17.5 - - - +
158H TYR* 3.2 18.6 - - - -
159H GLY* 3.4 21.9 - - - -
160H TYR* 5.1 0.2 - - - -
59I GLU* 5.1 6.4 + - - -
62I SER* 5.4 0.7 - - - -
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Residues in contact with MET 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H SER* 4.4 1.1 - - - -
135H PHE 3.3 12.1 - - - +
136H MET* 4.0 20.2 - - + -
149H TYR* 1.3 75.5 - - - +
151H ILE* 1.3 78.0 + - - +
152H ASP* 3.9 19.7 - - + +
156H VAL 3.3 3.6 - - - +
158H TYR* 2.8 54.3 + - + -
160H TYR* 3.9 27.1 - - + +
163H CYS* 4.6 6.5 - - - -
165H ILE* 4.1 23.8 - - + -
169H ARG* 5.7 4.5 - - - +
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Residues in contact with ILE 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H ALA* 4.0 34.5 - - + +
115H VAL* 5.2 0.4 - - + -
116H ALA* 4.0 10.3 - - + +
119H VAL* 4.1 16.8 - - + -
134H SER* 3.2 4.3 - - - -
135H PHE* 2.9 76.5 + - + +
137H LEU* 4.4 5.4 - - + -
149H TYR* 5.1 0.4 - - + -
150H MET* 1.3 85.9 - - - +
152H ASP* 1.3 74.5 + - - +
155H GLY* 4.4 6.1 - - - -
156H VAL 3.3 12.3 - - - +
157H SER* 3.8 12.3 - - - +
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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