Contacts of the strand formed by residues 164 - 171 (chain B) in PDB entry 3B94
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 TYR 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS* 4.2 18.4 - - + -
62B PHE 2.7 21.3 - - - +
63B GLY 3.7 15.0 - - - +
64B PRO* 3.7 8.1 - - + -
85B TRP* 4.1 6.1 - - - -
98B TYR* 4.0 18.6 - + - -
99B GLY* 3.1 20.1 - - - -
100B GLN* 2.7 74.8 + - + +
136B VAL* 4.4 1.4 - - - +
150B LEU* 5.0 1.4 - - - +
162B ASN 4.3 3.6 - - - -
163B THR* 1.3 81.8 - - - +
165B TRP* 1.4 67.0 + - - +
119C LYS* 5.9 0.5 + - - -
140C TYR* 4.5 7.1 - - - +
141C GLU* 3.9 39.7 + - + -
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Residues in contact with TRP 165 (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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61B LYS* 3.6 0.3 - - - +
62B PHE* 2.6 39.5 + - + +
69B TRP* 3.6 18.7 - + - -
85B TRP* 2.9 50.0 + + - +
87B LEU* 3.6 24.2 - - + -
97B ILE* 4.2 12.8 - - + -
98B TYR 3.3 11.4 - - - +
99B GLY* 3.7 2.0 - - - -
117B LEU* 5.1 2.7 - - + -
136B VAL* 3.8 17.5 - - + -
148B ILE* 3.5 40.4 - - + -
149B ASP* 4.5 0.4 - - - -
150B LEU* 3.7 26.5 - - + +
164B TYR* 1.4 83.8 - - - +
166B GLY* 1.4 84.2 + - - +
167B ILE* 4.2 13.2 - - + -
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Residues in contact with GLY 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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60B ALA 2.6 15.7 - - - -
61B LYS* 3.7 3.1 - - - -
69B TRP* 5.0 0.7 - - - -
97B ILE* 3.5 2.6 - - - -
98B TYR* 2.6 53.0 + - - +
165B TRP* 1.4 91.2 - - - +
167B ILE* 1.3 62.6 + - - -
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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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59B MET* 3.0 8.2 - - - +
60B ALA* 2.4 52.9 + - + +
78B CYS* 5.5 0.9 - - - -
79B VAL* 4.3 10.5 - - + -
87B LEU* 4.2 22.0 - - + -
89B ILE* 4.0 19.7 - - + -
95B TYR* 3.5 37.9 - - + -
96B LEU 3.6 10.8 - - - +
97B ILE* 4.1 12.6 - - + -
98B TYR* 3.2 5.0 - - - -
142B LEU* 4.1 7.0 - - + -
148B ILE* 5.2 0.9 - - + -
165B TRP* 4.2 11.2 - - + -
166B GLY* 1.3 74.7 - - - +
168B ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 4.2 14.4 - - + -
58B CYS 3.7 12.6 - - - +
59B MET* 4.0 14.4 - - + -
95B TYR* 3.4 5.5 - - - -
96B LEU* 2.7 65.0 + - + +
98B TYR* 5.1 0.2 - - + -
167B ILE* 1.3 78.9 - - - +
169B LEU* 1.4 70.5 + - - +
170B LEU* 4.2 12.3 - - + -
94C LEU* 4.2 21.8 - - + -
170C LEU* 4.8 8.7 - - + +
171C ALA* 4.0 27.1 - - + -
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Residues in contact with LEU 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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57B PRO* 4.8 8.0 - - - +
58B CYS* 3.2 26.1 + - + +
78B CYS* 4.2 14.1 - - + -
91B GLN* 4.1 18.8 - - - +
92B ASN 4.5 1.8 - - - +
93B GLY* 3.9 5.6 - - - -
94B LEU 3.8 8.7 - - - +
95B TYR* 3.4 43.7 - - + +
168B ILE* 1.4 83.1 - - - +
170B LEU* 1.3 60.8 + - - +
171B ALA 3.9 16.4 - - - +
172B ASN* 4.7 11.4 - - - +
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Residues in contact with LEU 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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57A PRO* 4.5 8.3 - - - +
96A LEU* 4.2 21.8 - - + -
168A ILE* 4.6 12.6 - - + +
170A LEU* 5.5 8.7 - - + -
94B LEU* 2.7 44.2 + - + +
96B LEU* 4.0 26.0 - - + +
139B THR* 4.7 2.7 - - - +
168B ILE* 3.6 23.5 + - + -
169B LEU* 1.3 74.8 - - - +
171B ALA* 1.3 60.2 + - + +
170C LEU* 5.0 11.4 - - + -
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Residues in contact with ALA 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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56A GLU* 5.7 1.8 - - - +
57A PRO* 4.2 4.5 - - + -
59A MET* 2.9 38.4 - - + -
168A ILE* 3.9 12.1 - - + -
93B GLY* 3.4 2.1 - - - -
94B LEU* 2.7 37.4 + - + +
169B LEU* 3.5 8.0 - - - +
170B LEU* 1.3 83.9 - - + +
172B ASN* 1.3 59.3 + - - +
173B PRO* 3.6 1.3 - - + -
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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