Contacts of the strand formed by residues 7 - 12 (chain E) in PDB entry 3QAZ
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 GLN 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E SER* 1.3 79.8 - - - +
8E PHE* 1.3 66.1 + - - +
9E THR* 3.7 19.3 + - - +
21E VAL* 4.1 1.1 - - - +
22E TRP* 3.9 3.0 - - - -
23E SER* 3.1 40.8 + - - +
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Residues in contact with PHE 8 (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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7E GLN* 1.3 82.0 - - - +
9E THR* 1.3 63.8 + - - +
10E CYS* 3.8 25.8 - - - -
20E CYS* 4.6 5.2 - - + -
21E VAL 3.6 11.4 - - - -
22E TRP* 3.9 12.1 - + + -
35E VAL* 4.5 14.6 - - + -
80E LEU* 3.9 27.8 - - + -
81E ARG 4.8 0.9 - - - -
82E VAL* 3.2 34.5 - - + -
94E ALA* 4.4 17.5 - - + -
95E ILE 5.2 1.1 - - - -
96E GLN* 3.1 51.0 + - + -
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Residues in contact with THR 9 (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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7E GLN* 3.7 23.5 + - - +
8E PHE* 1.3 77.8 + - - +
10E CYS* 1.3 67.7 + - - +
11E PHE* 4.1 31.9 - - + -
19E SER 3.9 0.2 - - - +
20E CYS* 3.6 1.0 - - - -
21E VAL* 2.9 50.6 + - + +
96E GLN* 5.0 0.4 - - - +
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Residues in contact with CYS 10 (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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8E PHE* 3.8 21.5 + - - -
9E THR* 1.3 77.6 - - - +
11E PHE* 1.3 80.4 + - - +
18E ILE* 4.1 8.1 - - + -
19E SER 2.9 6.5 - - - +
20E CYS* 2.0 47.1 - - - -
80E LEU* 3.9 22.7 - - + -
96E GLN* 4.9 5.2 + - - +
98E PHE* 3.6 18.6 - - + -
103E ASN* 4.2 1.6 - - - +
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Residues in contact with PHE 11 (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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9E THR* 4.1 21.8 - - + -
10E CYS* 1.3 91.2 - - - +
12E TYR* 1.3 62.1 + - - +
13E ASN 3.8 0.7 + - - -
18E ILE* 3.4 4.1 - - - -
19E SER* 2.8 39.1 + - - +
98E PHE* 4.6 0.4 - - - -
103E ASN* 4.2 22.2 - - + -
104E LEU 4.6 3.4 - - - -
105E ARG* 3.5 52.7 - - + +
191E PHE* 3.6 25.1 - - + -
193E THR* 4.4 20.6 - - + -
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Residues in contact with TYR 12 (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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11E PHE* 1.3 73.4 - - - +
13E ASN* 1.3 70.3 + - - +
14E SER* 3.2 32.1 + - - -
15E ARG* 3.1 37.8 + - - -
16E ALA 4.3 0.9 - - - -
17E GLN 3.2 14.4 - - - -
18E ILE* 3.8 13.5 - - + -
64E LEU* 4.8 2.5 - - + -
70E GLN* 4.1 1.4 + - - -
72E LEU* 3.8 36.2 + - + +
98E PHE* 4.0 10.1 - - + -
100E PRO* 3.3 37.2 - - + +
101E PHE* 3.5 21.5 - + - -
103E ASN 3.2 16.3 + - - +
104E LEU* 3.5 9.0 - - + +
105E ARG 3.0 23.3 + - - -
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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