Contacts of the strand formed by residues 143 - 149 (chain A) in PDB entry 6PSI
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 ARG 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A SER* 4.9 5.7 + - - -
59A ASP* 2.9 37.7 + - + +
62A LYS* 5.8 1.3 - - + -
79A PRO* 5.4 2.2 - - - -
84A ASP* 3.0 35.5 + - + -
86A SER* 2.7 30.8 + - - -
106A PHE* 5.7 6.3 - - + -
138A VAL 3.9 1.7 - - - +
139A GLU* 3.3 2.1 - - - -
140A VAL* 2.9 36.1 + - - +
141A ALA* 3.3 4.8 + - + +
142A GLY* 1.3 76.8 - - - +
144A ARG* 1.3 62.2 + - - +
145A VAL* 3.4 19.9 + - - +
161A VAL* 5.7 1.4 - - - +
162A PRO 3.7 0.4 + - - -
163A GLY* 3.2 10.4 - - - +
164A MET* 2.8 47.9 - - + +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.6 8.7 - - - +
60A PRO* 3.3 33.8 - - + +
61A GLU* 3.0 51.3 + - - +
137A VAL* 3.6 31.3 - - + +
138A VAL 3.5 3.6 - - - +
139A GLU* 2.9 46.0 + - + +
142A GLY 3.9 3.1 + - - +
143A ARG* 1.3 74.8 - - - +
145A VAL* 1.3 59.3 + - - +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 5.5 1.8 - - - +
59A ASP* 3.3 6.7 - - - +
60A PRO* 4.9 1.1 - - - -
136A ARG 3.1 2.3 - - - +
137A VAL* 3.6 3.7 - - - -
138A VAL* 2.9 60.4 + - + +
140A VAL* 6.1 0.2 - - + -
143A ARG* 3.4 38.9 - - - +
144A ARG* 1.3 74.6 - - - +
146A SER* 1.3 72.3 + - - +
147A VAL* 4.1 12.1 - - + +
161A VAL* 5.1 4.3 - - + -
164A MET* 3.9 30.3 - - + -
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 4.3 9.5 + - - +
54A TYR* 5.0 5.2 + - - -
58A SER* 3.7 29.7 + - - -
59A ASP* 4.0 4.2 + - - -
60A PRO* 4.6 8.7 - - - +
135A GLU* 3.2 31.9 - - - +
136A ARG 3.4 7.4 + - - -
137A VAL* 4.9 7.4 - - - +
144A ARG 4.1 1.0 + - - -
145A VAL* 1.3 78.3 - - - +
147A VAL* 1.4 59.5 + - - +
148A ARG 3.8 2.4 + - - -
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 5.0 1.1 - - + -
135A GLU* 4.3 0.2 - - - -
136A ARG* 2.8 33.9 + - + +
138A VAL* 3.6 31.6 - - + -
145A VAL* 3.7 14.3 - - + -
146A SER* 1.4 72.8 - - - +
148A ARG* 1.3 62.5 + - - +
149A ILE* 3.1 12.2 + - + +
159A ILE* 3.8 27.6 - - + -
161A VAL* 5.0 10.1 - - + -
176A LEU* 3.8 31.0 - - + -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.6 22.0 - - + +
27A LYS* 4.9 17.5 - - - +
133A GLY 4.8 2.4 + - - -
134A GLY* 3.2 31.3 - - - +
135A GLU* 2.9 34.8 + - + +
146A SER 3.8 3.8 + - - -
147A VAL* 1.3 75.4 - - - +
149A ILE* 1.3 66.6 + - - +
150A PRO* 3.9 3.5 - - - +
151A PRO* 4.8 16.3 - - - +
159A ILE* 4.6 4.9 - - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.5 9.4 - - + -
125A LEU* 3.8 40.4 - - + -
129A GLU* 3.2 33.2 - - + +
130A ALA* 4.4 2.5 - - - -
133A GLY* 4.2 2.7 - - - -
134A GLY 2.8 37.4 + - - +
136A ARG* 3.9 17.3 - - + +
147A VAL* 3.9 11.0 - - + +
148A ARG* 1.3 78.5 - - - +
150A PRO* 1.4 70.4 - - + +
151A PRO* 3.7 2.9 - - - +
153A VAL* 4.3 3.1 - - + -
159A ILE* 4.2 15.7 - - + -
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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