Contacts of the strand formed by residues 151 - 155 (chain J) in PDB entry 6AHU
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 ALA 151 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ASP 3.6 5.4 + - - +
124J LEU* 3.5 26.9 - - + -
125J VAL 3.1 19.5 + - - -
149J GLY 3.6 4.9 + - - +
150J LEU* 1.3 81.2 - - - +
152J PHE* 1.3 70.6 + - - +
184J ASN* 3.7 22.4 - - + +
186J ILE* 5.0 7.0 - - + -
224J ASN 5.0 0.9 - - - +
228J ALA* 4.0 15.5 - - + -
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Residues in contact with PHE 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 4.2 19.1 - + - -
117J CYS* 4.4 4.5 - - - -
124J LEU* 4.4 0.4 - - - -
125J VAL* 3.3 33.4 - - + +
127J ILE* 3.7 24.0 - - + -
142J ILE* 3.7 26.9 - - + -
145J ALA* 4.3 20.2 - - + -
146J ILE* 5.6 0.9 - - + -
150J LEU* 4.4 9.6 - - + -
151J ALA* 1.3 82.4 - - - +
153J GLU* 1.3 59.3 + - - +
154J LEU* 3.1 3.3 + - + +
176J LEU* 4.9 5.6 - - + -
180J CYS* 4.6 11.4 - - - -
184J ASN* 3.8 19.1 + - - +
185J VAL* 4.2 18.3 - - + +
186J ILE* 3.1 32.1 + - - +
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Residues in contact with GLU 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ASP* 2.9 35.4 - - - +
10J ARG* 3.8 7.4 + - - -
36J ASN* 4.4 8.2 + - - +
76J ARG* 4.0 8.3 + - - -
78J THR* 4.2 2.9 + - - -
102J VAL* 5.5 0.5 - - - +
104J ALA* 3.8 21.8 - - - +
124J LEU* 3.6 24.5 - - + +
125J VAL 2.9 11.7 + - - +
126J CYS* 3.2 23.6 - - - -
127J ILE* 3.2 22.6 + - - -
152J PHE* 1.3 68.2 - - - +
154J LEU* 1.3 60.3 + - - +
155J VAL* 3.1 21.2 + - + +
186J ILE* 3.8 8.7 - - + -
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Residues in contact with LEU 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J ILE* 3.7 29.6 - - + +
152J PHE* 3.1 4.2 + - + +
153J GLU* 1.3 67.4 - - - +
155J VAL* 1.3 64.4 + - - +
156J TYR* 3.4 4.9 + - - +
169J THR 5.5 0.9 - - - +
172J SER* 4.7 6.7 - - - +
173J ALA* 3.8 26.2 - - + -
176J LEU* 4.9 9.9 - - + -
177J MET* 4.9 6.3 - - + -
185J VAL* 4.1 22.4 - - + -
186J ILE* 3.0 19.5 + - - +
187J ILE* 3.6 23.2 - - + +
210J PHE* 3.6 34.7 - - + -
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Residues in contact with VAL 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ASP* 5.3 3.8 - - + +
10J ARG* 3.9 24.5 - - - +
127J ILE 4.2 1.4 + - - +
128J THR* 3.4 31.2 - - + +
153J GLU* 3.1 32.4 + - + +
154J LEU* 1.3 71.1 - - - +
156J TYR* 1.3 63.8 + - - +
157J SER* 4.1 3.1 + - - +
169J THR* 5.2 4.7 - - - +
188J SER* 3.3 25.8 - - - +
189J SER 4.6 0.2 - - - -
190J ALA* 3.9 30.3 - - + +
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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