Contacts of the strand formed by residues 169 - 175 (chain A) in PDB entry 5N4D
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 SER 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A VAL* 3.9 8.4 - - - +
160A ALA* 4.3 8.3 - - - -
161A VAL 3.3 14.1 - - - -
162A SER* 2.6 22.2 + - - -
168A TYR* 1.3 75.5 - - - +
170A THR* 1.3 63.6 + - - +
199A TRP 3.5 7.4 + - - -
200A PHE* 2.9 56.0 + - - +
201A LYS* 5.5 0.6 - - - +
698A HIS* 4.0 8.5 - - - +
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Residues in contact with THR 170 (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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159A TYR 3.6 0.9 - - - +
160A ALA* 3.3 0.9 - - - -
161A VAL* 2.8 33.5 + - - -
163A HIS* 5.8 4.3 - - - -
168A TYR 5.4 0.3 + - - -
169A SER* 1.3 76.9 + - - +
171A ILE* 1.3 66.2 + - - +
172A TYR* 3.4 40.5 + - + +
196A GLU* 3.5 23.1 + - + +
197A VAL 3.3 14.8 - - - +
198A LYS* 4.1 14.8 - - + +
199A TRP 5.0 0.2 + - - -
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Residues in contact with ILE 171 (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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158A ALA* 4.2 2.0 - - + -
159A TYR 3.4 14.1 - - - +
160A ALA* 4.3 4.7 - - + -
170A THR* 1.3 73.8 - - - +
172A TYR* 1.3 73.6 + - - +
173A VAL* 5.5 0.2 - - - -
195A ASP* 4.2 0.5 - - - +
196A GLU* 3.8 4.9 - - - -
197A VAL* 2.8 46.8 + - + +
200A PHE* 3.6 44.9 - - + -
205A ILE* 4.0 19.5 - - + -
214A PHE* 3.8 26.5 - - + -
216A TYR* 3.8 25.8 - - + -
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Residues in contact with TYR 172 (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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137A LEU* 6.2 0.2 - - + -
158A ALA* 3.2 4.3 - - - -
159A TYR* 2.9 57.0 + + + +
161A VAL* 3.8 27.8 - - + -
163A HIS* 5.2 7.2 + - - -
170A THR* 3.4 34.6 - - + +
171A ILE* 1.3 74.5 - - - +
173A VAL* 1.3 67.3 + - - +
192A ARG* 3.6 47.1 + - - -
195A ASP 3.6 8.7 - - - -
196A GLU* 3.0 33.0 + - + -
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Residues in contact with VAL 173 (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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156A PHE* 3.9 35.0 - - + -
157A PHE 3.4 8.7 - - - +
158A ALA* 4.6 2.2 - - + -
159A TYR* 4.2 0.2 - - - -
171A ILE 5.5 0.7 - - - +
172A TYR* 1.3 81.4 - - - +
174A ARG* 1.3 65.9 + - - +
192A ARG* 3.6 3.9 - - - +
193A LEU* 2.9 42.7 + - + +
195A ASP* 4.2 24.3 + - + +
197A VAL* 5.9 0.4 - - + -
207A TRP* 4.6 2.0 - - + -
214A PHE* 3.7 31.2 - - + -
239A HIS* 4.7 0.7 - - + -
241A VAL* 4.4 9.4 - - + -
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Residues in contact with ARG 174 (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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131A PHE* 4.7 4.6 - - - -
132A PHE* 3.8 18.4 - - - -
156A PHE* 3.5 8.1 - - - -
157A PHE* 2.9 38.6 + - + +
159A TYR* 3.1 37.6 + - + +
173A VAL* 1.3 74.8 - - - +
175A SER* 1.3 65.9 + - - +
178A SER* 2.5 40.9 + - - +
179A PRO 2.8 19.6 + - - -
180A LEU* 3.8 17.2 - - - +
190A ASP* 2.5 44.5 + - - -
191A GLY 4.9 1.1 - - - +
192A ARG* 3.6 12.1 - - + +
193A LEU* 4.4 2.2 - - - +
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Residues in contact with SER 175 (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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131A PHE* 4.0 2.1 - - - -
155A LYS 3.5 10.9 + - - -
156A PHE* 3.9 14.4 - - - -
174A ARG* 1.3 77.1 - - - +
176A THR* 1.3 61.2 + - - +
177A SER* 2.8 26.8 + - - -
178A SER* 3.0 36.8 + - - +
191A GLY 5.1 2.9 + - - -
193A LEU* 5.2 4.9 - - - +
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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