Contacts of the strand formed by residues 117 - 123 (chain B) in PDB entry 1QN7
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 ASN 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASN 4.0 0.3 - - - +
28B ILE* 3.5 2.9 - - - +
29B VAL* 2.9 38.5 + - + +
115B ILE* 3.7 1.2 - - - +
116B GLN* 1.3 80.9 - - - +
118B ILE* 1.3 66.1 + - - +
119B VAL* 3.7 10.0 - - - +
173B THR* 3.4 2.2 + - - -
174B GLY* 2.9 35.6 + - - -
175B ALA 3.3 6.2 + - - -
206E A 3.3 28.0 + - - -
207E T 3.1 42.5 + - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.9 25.6 - - + -
27B ASN 3.7 3.1 - - - -
28B ILE* 3.7 18.4 - - + -
87B GLU* 3.9 16.2 - - + +
115B ILE* 3.7 17.9 - - + -
117B ASN* 1.3 77.9 + - - +
119B VAL* 1.3 65.6 + - - +
172B ILE 3.8 1.2 - - - +
173B THR* 3.6 3.5 - - - -
174B GLY 3.5 18.4 + - - -
175B ALA* 2.8 25.1 + - + +
176B LYS 3.9 3.6 - - - +
177B MET* 3.6 14.1 - - - +
178B ARG* 3.4 30.3 - - - +
181B THR* 3.9 8.9 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.6 4.3 - - - +
26B GLN* 2.7 36.6 + - + -
27B ASN* 2.9 25.3 + - + +
29B VAL* 5.7 0.2 - - + -
117B ASN* 3.7 9.9 - - - +
118B ILE* 1.3 77.9 - - - +
120B GLY* 1.3 56.6 + - - +
171B VAL* 4.0 12.8 - - + -
172B ILE 3.5 4.5 - - - +
173B THR* 3.4 20.0 - - - +
206E A 3.6 8.1 - - + -
223F T 3.5 21.1 - - - +
224F A 3.7 29.2 - - + +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR 3.0 17.3 - - - -
25B LEU* 4.1 2.0 - - - -
26B GLN* 4.1 3.4 - - - -
118B ILE 4.2 0.2 - - - -
119B VAL* 1.3 75.6 - - - +
121B SER* 1.3 63.2 + - - -
171B VAL* 3.4 7.4 - - - +
172B ILE* 2.8 36.0 + - - +
181B THR* 4.7 14.3 - - - +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PRO* 3.3 2.1 - - - +
24B THR* 2.8 32.9 + - - +
26B GLN* 2.9 29.0 + - - +
120B GLY* 1.3 75.9 - - - -
122B CYS* 1.3 63.8 + - - +
170B ILE 3.0 17.9 - - - -
171B VAL* 4.2 1.1 - - - +
172B ILE* 4.4 2.4 - - - +
224F A 4.0 28.2 + - - -
225F T 5.2 3.5 - - - -
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Residues in contact with CYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 4.2 11.4 - - + -
22B VAL 4.6 2.0 - - - +
23B PRO* 3.7 23.6 - - + -
24B THR* 5.6 0.4 - - - -
121B SER* 1.3 78.0 - - - +
123B ASP* 1.3 63.5 + - - +
169B LYS* 3.5 6.9 - - - +
170B ILE* 2.8 36.2 + - - +
172B ILE* 4.2 6.5 - - - -
185B PHE* 3.5 41.5 - - - -
225F T 5.8 0.3 - - - +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 4.2 17.0 - - - +
122B CYS* 1.3 81.3 - - - +
124B VAL* 1.3 62.9 + - - +
125B LYS* 2.8 62.7 + - - +
126B PHE 4.5 0.2 + - - -
167B SER 4.5 1.0 - - - +
168B GLY* 3.3 16.6 - - - +
169B LYS* 3.1 35.4 + - + -
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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