Contacts of the strand formed by residues 123 - 128 (chain F) in PDB entry 5A2Q
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 GLU 123 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F PRO* 4.2 0.9 - - - +
122F ARG* 1.3 90.1 + - + +
124F ASP* 1.3 64.0 + - - +
138F ALA* 5.5 2.7 - - + -
139F VAL 3.4 13.5 - - - +
140F ASP* 4.2 13.3 - - + +
141F VAL* 4.2 0.7 - - - -
196F LEU* 4.1 20.4 - - - +
197F GLU* 4.2 7.1 + - + +
200F ALA* 3.8 21.3 - - + +
204F ARG* 2.8 24.2 + - - -
44c ARG* 5.5 0.3 + - - -
57c THR 5.4 1.3 - - - +
58c LEU* 5.2 0.2 - - - -
59c LEU* 3.2 40.9 + - + +
60c GLU* 3.2 28.6 + - - +
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Residues in contact with ASP 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F PRO* 4.7 2.6 - - - +
123F GLU* 1.3 75.3 - - - +
125F SER* 1.3 79.9 + - - +
138F ALA* 3.7 3.1 - - - -
139F VAL* 2.9 38.0 + - + +
141F VAL* 4.1 16.2 - - + +
145F ARG* 4.8 0.9 + - - -
149F GLN* 3.5 16.3 + - - -
196F LEU* 3.3 44.7 - - - +
200F ALA* 5.0 2.0 - - - -
47c LYS* 4.2 23.8 + - + +
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Residues in contact with SER 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ASP* 1.3 89.8 + - - +
126F THR* 1.3 63.0 + - - +
127F ARG 4.1 0.7 + - - -
136F ARG* 3.6 34.8 - - - -
137F GLN 3.5 6.5 - - - -
139F VAL* 5.4 0.2 - - - -
196F LEU* 4.3 2.3 + - - -
199F VAL* 3.3 25.3 - - - +
200F ALA* 3.8 10.0 + - - -
203F ASN* 4.0 3.8 + - - -
47c LYS* 4.1 12.6 + - - -
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP 4.0 0.8 + - - -
125F SER* 1.3 73.6 + - - +
127F ARG* 1.3 69.5 + - - +
128F ILE* 3.3 8.0 + - + +
136F ARG* 4.2 1.8 - - - -
137F GLN* 2.9 33.9 + - - -
139F VAL* 4.4 4.9 - - - +
26c GLN* 3.3 38.3 + - + +
27c CYS* 3.8 19.2 - - - -
47c LYS* 4.2 19.4 - - - +
68c LEU* 4.2 16.6 - - + -
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12202 A 5.7 4.9 - - - +
125F SER 4.1 1.4 + - - -
126F THR* 1.3 72.1 - - - +
128F ILE* 1.3 66.7 + - - +
129F GLY 5.5 0.6 - - - +
130F ARG 2.8 18.7 + - - -
131F ALA* 3.2 9.9 - - - +
132F GLY* 2.8 34.1 - - - +
133F THR 3.2 15.0 + - - +
134F VAL* 3.5 36.5 - - + +
135F ARG 4.6 0.2 - - - +
136F ARG* 4.1 15.6 - - + +
23c SER* 5.4 2.1 - - - -
24c GLN* 4.6 6.1 - - - +
26c GLN* 3.8 22.6 + - - +
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Residues in contact with ILE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F THR* 3.4 13.9 - - + +
127F ARG* 1.3 82.8 - - - +
129F GLY* 1.3 62.0 + - - +
133F THR 4.0 1.2 - - - +
135F ARG* 2.6 47.3 + - + +
137F GLN* 3.4 39.7 - - + +
23c SER* 6.1 6.1 - - - -
26c GLN* 5.8 0.7 - - - +
66c ARG* 5.0 9.2 - - - +
68c LEU* 3.8 37.2 - - + +
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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