Contacts of the strand formed by residues 124 - 130 (chain E) in PDB entry 2QXU
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 LEU 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E ALA 3.0 8.4 + - - +
98E ASN* 3.6 23.1 - - + +
99E VAL* 2.9 30.0 + - - +
121E GLN* 3.9 17.3 - - - +
122E LYS* 3.8 14.8 - - + +
123E ILE* 1.3 74.7 - - - +
125E TYR* 1.3 61.4 + - - +
172E GLY 5.9 0.2 - - - +
175E GLY* 4.3 17.3 - - - +
177E GLY* 3.9 22.0 - - - +
178E GLN* 3.8 22.7 - - - -
179E ASN* 3.9 7.0 - - + +
124F LEU* 6.3 5.8 - - + -
175F GLY 5.5 5.4 - - - +
177F GLY 5.6 2.9 - - - +
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Residues in contact with TYR 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 3.7 21.3 - - + +
87E ILE* 3.5 20.1 - - + +
99E VAL* 3.4 32.3 - - + -
101E THR* 5.7 1.8 - - + -
113E ALA* 3.6 17.7 - - + -
114E LEU* 2.6 42.6 + - - +
123E ILE* 3.4 28.0 - - + +
124E LEU* 1.3 74.7 - - - +
126E THR* 1.3 65.4 + - - +
127E SER* 6.0 0.2 - - - -
143E LEU* 4.1 15.7 - - + -
146E ALA* 3.5 19.1 - - + -
147E ARG* 3.1 16.1 + - - +
177E GLY* 4.0 0.2 - - - -
178E GLN 3.0 26.5 + - - +
179E ASN* 3.6 4.7 - - - -
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Residues in contact with THR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL 3.0 10.2 + - - -
100E VAL* 3.3 11.7 - - + +
101E THR* 3.0 23.5 + - - -
125E TYR* 1.3 70.8 - - - +
127E SER* 1.3 58.7 + - - +
128E ILE* 3.6 28.0 - - + -
147E ARG* 3.2 25.6 - - - +
149E VAL* 4.4 1.6 - - + -
168E LEU* 4.6 10.1 - - + +
172E GLY* 3.6 17.3 - - - -
176E GLY 4.1 1.9 + - - -
177E GLY* 3.1 25.6 + - - -
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E THR* 3.4 17.9 + - - -
106E ASN* 3.7 1.7 + - - -
125E TYR* 4.1 0.8 - - - -
126E THR* 1.3 71.5 - - - +
128E ILE* 1.3 56.9 + - - +
129E TYR* 3.4 9.8 - - - -
141E SER* 2.5 32.2 + - - -
143E LEU* 4.9 9.0 - - - -
146E ALA* 5.0 2.4 - - - +
147E ARG 2.8 8.7 + - - -
148E ASN* 3.5 21.4 - - - -
149E VAL 2.8 30.7 + - - -
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E VAL* 4.4 11.0 - - + -
101E THR 2.9 14.9 + - - +
102E LEU* 3.4 8.6 - - + -
103E GLY 2.7 25.3 + - - -
104E GLY 4.6 0.3 + - - -
126E THR* 3.6 26.0 - - + -
127E SER* 1.3 72.6 + - - +
129E TYR* 1.3 64.5 + - - +
149E VAL* 3.4 31.6 - - + +
151E ILE* 4.4 19.1 - - + -
159E LEU* 5.1 3.2 - - + +
165E VAL* 4.6 14.1 - - + -
168E LEU* 3.6 36.6 - - + -
169E ILE 5.5 0.4 - - - +
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Residues in contact with TYR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E GLY* 4.3 8.1 - - - +
127E SER* 3.4 29.6 - - - -
128E ILE* 1.3 77.7 - - - +
130E SER* 1.3 59.9 + - - +
133E ASP* 6.0 0.2 - - - +
138E ASN* 3.4 33.9 - - + +
141E SER* 3.7 25.8 - - - +
142E ARG* 2.7 42.7 + - + -
148E ASN* 3.7 8.4 + - + +
149E VAL 3.1 10.3 + - - -
150E GLN* 3.3 46.0 + - + +
151E ILE* 2.8 29.9 + - - +
159E LEU* 5.0 2.9 - - - -
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Residues in contact with SER 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TYR* 1.3 75.9 - - - +
131E SER* 1.3 58.5 + - - +
132E ALA* 2.9 13.5 + - - +
133E ASP* 3.0 28.0 + - - +
138E ASN* 2.9 17.4 - - - +
151E ILE* 3.3 20.6 + - - -
152E HIS 4.0 0.2 - - - -
153E GLY 4.0 0.9 + - - -
154E VAL 2.7 35.1 + - - -
159E LEU* 4.2 13.0 - - - +
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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