Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 3A7N
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.4 1.6 - - + -
61A ARG 3.5 22.4 - - - +
62A VAL 4.2 1.1 - - - +
63A LEU* 4.1 17.5 - - + +
156A LEU* 4.1 39.5 - - + +
157A ALA* 4.6 8.5 - - - +
159A ARG* 4.2 13.7 - - - +
161A ALA 4.6 2.5 - - - +
162A PRO* 1.3 75.3 - - - +
164A VAL* 1.3 69.6 + - - +
165A ALA* 5.2 0.7 - - + -
179A LEU* 3.7 29.8 - - + -
183A ASN 3.0 10.0 + - - +
184A CYS* 3.2 13.1 - - + -
185A VAL 3.1 23.6 + - - -
214A LEU* 4.9 0.4 - - - -
217A MET* 3.8 4.9 - - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG 2.9 11.7 + - - +
62A VAL* 3.2 12.6 - - + +
63A LEU* 2.8 31.2 + - - +
163A LEU* 1.3 73.8 - - - +
165A ALA* 1.3 59.5 + - - +
166A ILE* 4.4 3.4 - - + -
185A VAL 3.4 9.4 - - - +
187A ILE* 3.8 29.2 - - + -
210A ALA* 3.7 30.7 - - + +
213A LEU* 3.8 12.1 - - + -
214A LEU* 4.0 7.9 - - + -
217A MET* 3.7 24.9 - - + -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.6 16.4 - - + -
163A LEU* 4.1 1.4 + - + -
164A VAL* 1.3 71.7 - - - +
166A ILE* 1.3 58.6 + - - +
167A LEU* 3.6 12.3 + - + +
179A LEU* 3.6 31.9 - - + -
184A CYS* 4.1 10.8 - - - -
185A VAL 3.0 8.2 + - - +
186A ALA* 3.2 6.2 - - - +
187A ILE 2.8 31.9 + - - +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.8 25.6 - - + -
63A LEU 2.7 19.6 + - - +
64A ILE* 3.9 19.1 - - + +
65A VAL 3.8 16.6 + - - +
164A VAL* 4.4 2.2 - - + -
165A ALA* 1.3 72.0 - - - +
167A LEU* 1.3 62.5 + - - +
168A TRP* 3.2 44.0 + - + +
187A ILE* 3.6 24.5 - - + +
206A PRO* 4.1 28.5 - - + +
207A PHE* 5.1 2.9 - - + -
210A ALA* 4.3 5.6 - - + -
224A TRP* 4.3 6.5 - - + -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 5.1 3.4 - - + -
65A VAL* 3.6 21.3 - - + -
165A ALA* 4.0 20.6 - - + +
166A ILE* 1.3 73.4 - - - +
168A TRP* 1.3 62.7 + - - +
169A GLY 3.8 2.7 + - - +
172A ALA* 3.5 35.2 - - + +
173A SER* 4.2 5.5 - - - +
175A LEU* 4.7 3.4 - - + -
176A LYS* 3.5 35.2 - - + +
179A LEU* 4.5 10.8 - - + -
186A ALA* 4.0 13.0 - - + -
187A ILE 2.7 13.2 + - - +
188A GLU* 3.5 10.2 - - + +
189A SER 3.3 24.4 + - - +
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Residues in contact with TRP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.5 34.1 - - + -
65A VAL 4.7 6.7 + - - +
67A GLN* 4.1 5.4 + - - -
81A PHE* 3.6 30.1 - + - -
97A ILE* 3.6 33.7 - - + -
118A TRP* 5.6 1.6 - + - -
166A ILE* 3.2 32.8 + - + +
167A LEU* 1.3 73.0 - - - +
169A GLY* 1.3 61.0 + - - +
172A ALA* 3.4 16.5 - - - +
187A ILE* 5.4 1.7 - - + +
189A SER* 3.2 23.8 + - - -
190A PRO 4.1 0.2 - - - -
191A HIS* 3.4 18.0 - - + -
192A PRO* 3.6 24.2 - - + -
201A PHE* 3.4 27.4 - + - -
204A SER* 5.2 0.2 + - - -
206A PRO* 4.4 16.7 - - + +
207A PHE* 4.7 7.2 - + - -
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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