Contacts of the strand formed by residues 165 - 174 (chain B) in PDB entry 5AEW
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.9 2.0 - - + -
26B GLU* 3.8 42.4 - - + -
27B ILE* 3.6 28.9 - - + -
30B PHE* 3.4 49.5 - + + -
49B LEU* 3.7 3.6 - - - +
128B PHE* 4.1 10.3 - + - -
156B LEU* 4.3 10.8 - - + -
157B ARG* 3.2 18.2 - - - +
158B ARG* 3.8 27.4 - - + -
159B ALA* 3.9 2.5 - - - +
161B ASN* 2.9 19.7 + - - +
163B LEU 3.4 5.6 - - - -
164B GLY* 1.3 95.7 - - - +
166B SER* 1.3 62.5 + - - +
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Residues in contact with SER 166 (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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48B ALA 5.6 0.7 - - - -
49B LEU 3.2 14.8 - - - -
51B ASP* 2.7 37.5 + - - -
156B LEU* 3.4 7.4 - - - +
157B ARG* 2.9 41.8 + - - +
159B ALA* 3.8 12.9 - - - +
161B ASN* 4.3 4.0 - - - -
165B PHE* 1.3 74.1 - - - +
167B ILE* 1.3 65.2 + - - +
168B ALA 3.8 0.2 + - - -
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Residues in contact with ILE 167 (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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30B PHE* 4.0 16.8 - - + -
34B GLU* 3.9 12.8 - - - +
46B TRP* 4.8 1.6 - - - +
49B LEU* 2.8 20.7 + - + +
50B LEU* 4.0 17.5 - - + -
51B ASP* 3.0 25.5 + - - +
54B ILE* 3.5 26.3 - - + +
154B ASP* 4.8 0.4 - - - -
155B VAL 3.8 4.3 - - - +
156B LEU* 3.9 17.0 - - + -
166B SER* 1.3 73.9 - - - +
168B ALA* 1.3 59.9 + - - +
169B LYS 3.7 21.5 - - - +
170B ARG* 3.6 34.8 - - + +
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Residues in contact with ALA 168 (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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51B ASP* 4.1 7.2 - - - +
53B ASP* 3.7 7.3 - - - +
54B ILE* 3.2 24.0 - - - +
55B HIS* 3.5 2.4 + - - +
155B VAL* 2.8 26.7 + - + +
157B ARG* 3.4 43.5 - - + +
166B SER 3.8 1.8 + - - -
167B ILE* 1.3 73.7 - - - +
169B LYS* 1.3 63.1 + - + +
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Residues in contact with LYS 169 (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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54B ILE* 4.6 0.7 - - - -
55B HIS* 3.5 29.2 - - + +
153B ARG* 5.2 4.6 + - - +
154B ASP* 3.1 7.6 - - - +
155B VAL* 2.8 52.3 + - + +
167B ILE* 3.5 7.2 - - - +
168B ALA* 1.3 82.4 - - + +
170B ARG* 1.3 66.0 + - - +
171B THR* 4.1 17.0 + - - +
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Residues in contact with ARG 170 (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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31B TYR* 3.7 4.4 - - - -
34B GLU* 2.6 42.0 + - - -
46B TRP* 4.2 9.9 - - - -
54B ILE* 5.0 1.0 - - + +
55B HIS 3.0 12.0 + - - +
56B TYR* 3.4 27.5 - - + -
57B PHE* 2.9 25.3 + - - +
152B ARG* 3.6 15.7 - - + +
153B ARG 3.5 5.4 - - - -
154B ASP* 2.9 37.0 + - - +
167B ILE* 3.6 27.1 - - + +
169B LYS* 1.3 75.8 - - - +
171B THR* 1.3 65.8 + - - +
172B ILE* 3.8 25.4 - - + -
188B PHE 3.5 20.9 + - - -
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Residues in contact with THR 171 (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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9B PHE* 3.8 33.1 - - + -
55B HIS* 6.0 0.2 + - - -
57B PHE* 3.1 26.2 - - + +
59B PRO* 4.4 0.9 - - + -
151B GLU 4.0 0.3 - - - +
152B ARG* 3.4 4.5 - - - +
153B ARG* 2.8 46.2 + - + +
169B LYS* 4.1 17.1 + - - +
170B ARG* 1.3 74.7 + - - +
172B ILE* 1.3 65.6 + - - +
173B LEU* 3.8 16.9 + - + -
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Residues in contact with ILE 172 (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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56B TYR* 3.8 37.7 - - + +
57B PHE 2.8 18.4 + - - +
58B MET* 3.6 37.5 - - + +
59B PRO* 3.3 21.7 - - - +
134B PHE* 3.8 32.1 - - + -
151B GLU 3.5 3.1 - - - -
152B ARG* 4.2 8.3 - - + -
170B ARG* 3.8 17.9 - - + -
171B THR* 1.3 73.5 - - - +
173B LEU* 1.3 68.0 + - - +
174B LEU* 3.7 3.1 + - + +
188B PHE* 3.8 15.5 - - + -
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Residues in contact with LEU 173 (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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9B PHE* 3.8 33.7 - - + -
59B PRO* 4.0 4.9 - - + -
61B ARG* 4.7 3.1 - - - +
73B TYR* 3.8 40.2 - - + +
150B GLY* 3.2 4.3 - - - -
151B GLU* 2.8 68.3 + - + +
153B ARG* 4.0 14.6 - - - +
171B THR* 3.8 26.2 - - + +
172B ILE* 1.3 74.6 - - - +
174B LEU* 1.3 60.5 + - - +
175B ASP* 4.4 2.6 - - - +
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Residues in contact with LEU 174 (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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58B MET* 4.0 31.3 - - + +
59B PRO 5.5 3.9 + - - +
61B ARG* 3.2 22.4 + - - +
73B TYR* 5.6 0.4 - - - -
81B HIS* 5.0 2.9 - - + -
134B PHE* 4.0 8.7 - - + -
148B PHE* 4.0 26.5 - - + -
149B ALA 3.5 16.2 - - - +
150B GLY* 4.5 0.2 - - - -
172B ILE* 3.7 4.4 + - + -
173B LEU* 1.3 73.7 - - - +
175B ASP* 1.3 60.6 + - - +
176B ALA* 2.9 20.5 + - + +
179B LEU* 4.1 25.8 - - + -
184B LEU* 4.8 5.8 - - + -
188B PHE* 3.9 24.7 - - + -
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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