Contacts of the strand formed by residues 165 - 171 (chain A) in PDB entry 3L4U
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 PHE 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO* 4.6 5.2 - - + -
46A TYR* 4.6 3.1 - - - -
77A VAL* 6.2 0.4 - - + -
78A PHE* 3.6 46.7 - + + -
160A LEU* 3.8 32.2 - - + +
161A PHE* 3.7 3.1 + - - -
162A ALA* 2.8 39.1 + - + +
164A GLN* 1.3 79.2 - - - +
166A LEU* 1.3 62.4 + - - +
167A GLN* 3.7 13.5 - - + -
254A ARG* 3.6 29.4 - - + -
255A THR 3.5 4.9 - - - -
256A ILE* 5.0 0.2 - - + -
468A PHE* 3.5 41.1 - + + -
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Residues in contact with LEU 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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108A ARG* 4.0 3.4 - - - +
160A LEU 3.3 7.6 - - - +
161A PHE* 3.7 38.6 - - + -
162A ALA 3.3 20.0 - - - +
163A ASP 4.1 0.2 - - - +
165A PHE* 1.3 80.1 - - - +
167A GLN* 1.3 61.1 + - - +
253A TYR 3.9 0.2 - - - +
254A ARG* 3.3 4.5 - - - +
255A THR* 2.9 43.4 + - + +
257A GLY* 3.6 36.3 - - - +
258A GLY 3.4 19.7 - - - +
259A ILE* 4.0 8.7 - - - -
260A LEU* 4.2 14.6 - - + -
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Residues in contact with GLN 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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13A ILE* 3.7 21.5 - - - +
14A ASN 4.9 0.8 + - - +
17A PRO* 5.6 0.8 - - - +
46A TYR* 4.0 12.4 + - - -
158A PRO* 3.7 6.0 - - - +
159A LEU* 3.6 6.1 - - - +
160A LEU* 3.0 52.4 + - + +
165A PHE* 3.7 14.5 - - + -
166A LEU* 1.3 76.3 - - - +
168A LEU* 1.3 66.2 + - - +
169A SER* 4.3 1.3 + - - +
252A THR* 3.4 22.1 - - + +
253A TYR 3.2 14.6 - - - +
254A ARG* 3.1 35.4 + - - +
260A LEU* 4.1 4.4 - - - +
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Residues in contact with LEU 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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99A PHE* 4.0 15.0 - - + -
101A LEU* 4.4 7.9 - - + -
138A PHE* 4.8 6.7 - - + -
140A ILE* 4.8 2.0 - - + -
152A PHE* 4.0 22.7 - - + -
154A SER* 3.8 20.6 - - - +
158A PRO 4.1 7.2 - - - +
159A LEU* 4.0 33.4 - - + +
167A GLN* 1.3 75.2 - - - +
169A SER* 1.3 68.3 + - - +
251A ILE 4.3 0.2 - - - +
252A THR* 3.6 0.8 - - - -
253A TYR* 3.0 34.9 + - - +
260A LEU* 4.1 11.7 - - + +
262A PHE* 3.8 28.3 - - + -
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Residues in contact with SER 169 (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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13A ILE* 3.9 17.7 - - - +
152A PHE* 4.5 2.2 - - - -
154A SER* 3.1 27.1 + - - -
156A ILE* 3.6 21.5 - - - -
157A GLY* 4.5 8.9 - - - -
158A PRO* 4.5 4.5 + - - +
167A GLN* 4.3 2.1 + - - +
168A LEU* 1.3 79.6 - - - +
170A THR* 1.3 63.2 + - - +
250A ALA* 5.7 0.4 - - - -
251A ILE 3.2 7.0 - - - -
252A THR* 2.8 30.0 + - - +
253A TYR* 6.4 0.2 - - - -
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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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151A LEU 4.0 0.2 + - - -
152A PHE* 3.2 33.9 - - + -
153A ASP 2.9 24.9 + - - -
156A ILE* 4.2 1.8 - - - -
169A SER* 1.3 75.6 - - - +
171A ARG* 1.3 80.2 + - - +
172A LEU* 4.1 6.5 - - + -
220A PHE* 4.8 6.1 - - + -
231A PHE* 6.3 0.2 - - + -
233A VAL* 5.5 0.2 - - + -
250A ALA* 3.2 5.3 - - - -
251A ILE* 2.8 61.0 + - + +
253A TYR* 5.6 4.3 - - + -
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Residues in contact with ARG 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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11A GLU* 3.1 30.0 + - - -
150A VAL* 5.8 2.7 - - + -
151A LEU 3.3 11.4 - - - +
153A ASP* 2.7 41.3 + - + +
155A SER* 2.6 27.5 + - - -
156A ILE* 3.4 41.1 - - + +
170A THR* 1.3 90.0 + - - +
172A LEU* 1.3 64.5 + - - +
248A ALA* 5.8 0.4 - - + -
249A PRO 3.6 9.0 - - - +
250A ALA* 4.2 2.2 - - - -
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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