Contacts of the strand formed by residues 163 - 172 (chain I) in PDB entry 5BRR
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I LEU* 5.6 1.6 - - + -
97I ILE* 4.4 14.6 - - + -
98I PHE 3.5 15.9 - - - +
99I VAL* 3.9 19.1 - - + -
121I VAL* 5.9 0.9 - - + -
126I PHE* 3.7 0.2 - - - -
162I ARG* 1.3 79.1 - - - +
164I VAL* 1.3 64.5 + - - +
306I PHE* 3.2 42.2 - - + -
309I LEU* 4.8 10.3 - - + -
315I LEU* 4.1 18.4 - - + -
316I HIS 3.2 18.8 + - - +
317I VAL* 3.3 20.0 - - + -
318I ALA* 3.0 26.4 + - - +
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Residues in contact with VAL 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ILE* 3.8 3.1 - - - -
98I PHE* 2.9 39.9 + - + +
126I PHE* 4.3 10.5 - - + -
136I ILE* 4.0 27.6 - - + -
154I THR* 6.2 0.4 - - + -
157I VAL* 4.7 3.4 - - + -
161I THR* 3.6 24.9 - - + -
162I ARG 4.3 0.2 - - - -
163I LEU* 1.3 80.2 - - - +
165I LEU* 1.3 63.4 + - - +
166I VAL* 4.5 9.6 - - + -
317I VAL* 5.3 0.4 - - - -
319I LEU* 3.5 43.5 - - + +
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Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 3.7 31.4 - - + +
43I LEU* 4.4 20.9 - - + -
46I LEU* 3.7 30.7 - - + -
96I ALA 3.8 4.0 - - - +
97I ILE* 3.8 27.1 - - + +
164I VAL* 1.3 74.3 - - - +
166I VAL* 1.3 74.4 + - - +
286I LEU* 5.8 2.2 - - + -
290I LEU* 5.9 0.2 - - + -
298I MET* 5.4 2.5 - - + -
317I VAL* 5.1 4.5 - - + -
319I LEU 3.1 12.4 + - - +
320I ALA* 3.3 20.1 - - + -
321I LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 3.8 3.8 - - - +
94I THR* 4.8 4.0 - - + -
95I ASP* 3.5 1.6 - - - -
96I ALA* 2.9 44.0 + - + +
98I PHE* 4.4 13.5 - - + -
136I ILE* 4.3 20.4 - - + -
139I TRP* 5.9 1.3 - - + -
140I VAL* 4.2 25.4 - - + -
151I LEU* 4.2 15.3 - - + -
154I THR* 5.7 2.7 - - + -
164I VAL* 4.5 10.3 - - + -
165I LEU* 1.3 84.1 - - - +
167I ASN* 1.3 73.0 + - - +
168I ALA* 4.9 0.7 - - + +
319I LEU* 6.5 0.4 - - + -
321I LEU* 3.7 11.4 - - + +
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Residues in contact with ASN 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLY* 3.1 28.1 + - - +
39I VAL* 5.4 0.4 - - - -
42I VAL* 3.9 15.0 - - + -
93I THR* 4.6 3.8 + - - -
94I THR 2.7 13.6 + - - -
95I ASP* 2.7 30.1 + - - -
151I LEU* 6.0 0.3 - - - +
166I VAL* 1.3 80.8 - - - +
168I ALA* 1.3 63.5 + - - +
169I LEU* 3.8 4.9 - - - +
286I LEU* 6.1 1.1 - - + -
321I LEU 3.1 10.9 + - - +
322I GLN* 2.6 39.0 + - + +
323I LYS 2.9 22.7 + - - -
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Residues in contact with ALA 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER 3.9 0.2 - - - +
93I THR 3.4 2.3 - - - -
94I THR* 3.0 46.4 + - + +
140I VAL* 4.0 26.2 - - + -
144I THR* 4.2 6.0 - - + +
148I ILE* 4.4 3.4 - - + -
151I LEU* 5.7 0.7 - - + -
166I VAL* 5.2 1.1 - - + -
167I ASN* 1.3 76.0 - - - +
169I LEU* 1.3 67.3 + - - +
323I LYS* 3.2 21.3 - - + +
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Residues in contact with LEU 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I SER* 3.3 39.7 - - - +
37I TYR* 4.6 11.4 - - + -
38I GLY* 4.2 1.3 - - - -
82I LEU* 6.5 0.7 - - + -
91I ILE* 5.0 6.1 - - + +
92I SER 3.2 9.4 - - - +
93I THR* 3.0 31.6 - - - +
144I THR* 4.9 1.3 - - - -
148I ILE* 4.0 5.2 - - - +
167I ASN* 3.8 16.2 - - - +
168I ALA* 1.3 82.3 - - - +
170I TYR* 1.3 60.4 + - - +
171I PHE 4.2 0.2 - - - -
323I LYS 3.3 5.5 + - - +
324I VAL* 3.5 14.8 - - + +
325I LYS 2.9 25.1 + - - +
371I LEU* 6.2 2.2 - - + -
372I PHE* 3.7 21.0 - - + -
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Residues in contact with TYR 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I ASP 4.8 11.0 - - - -
90I GLU 4.8 0.9 - - - -
91I ILE* 1.9 37.2 + - - +
92I SER* 3.4 10.9 + - - +
144I THR* 4.6 8.6 - - - +
145I LYS* 6.4 0.2 - - + -
147I MET* 3.6 56.3 - - + +
148I ILE* 4.5 10.5 - - + +
169I LEU* 1.3 74.9 - - - +
171I PHE* 1.3 59.4 + - - +
172I ASN* 2.9 42.5 + - + +
325I LYS* 3.3 36.1 - - + -
327I GLU* 3.8 23.0 + - + -
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Residues in contact with PHE 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I GLU* 2.9 32.8 - - + -
91I ILE* 4.1 11.7 - - + -
169I LEU 4.2 0.6 + - - -
170I TYR* 1.3 77.2 - - - +
172I ASN* 1.3 79.4 + - - +
228I TYR* 3.4 51.4 - + - -
233I LEU* 3.8 21.5 - - + -
325I LYS 2.7 13.2 + - - +
326I ILE* 3.3 21.3 - - + +
327I GLU* 2.8 28.3 + - - +
362I VAL* 3.8 13.0 - - + -
372I PHE* 3.4 34.8 - + + -
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Residues in contact with ASN 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I ASP 5.5 1.1 - - - +
90I GLU* 2.8 20.0 + - + +
170I TYR* 2.9 33.0 + - + +
171I PHE* 1.3 87.2 - - - +
173I GLY* 1.3 86.5 + - - +
327I GLU* 3.2 29.8 + - - +
329I ASN* 3.6 18.3 + - - +
331I SER 3.4 21.9 + - - +
332I GLY* 6.1 0.2 - - - -
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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