Contacts of the strand formed by residues 152 - 158 (chain B) in PDB entry 2W7W
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 THR 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B VAL* 3.4 0.3 - - - -
128B LYS* 2.9 50.2 + - - -
150B GLY 4.3 5.4 + - - -
151B VAL* 1.3 76.5 - - - +
153B PRO* 1.4 77.2 - - + +
154B LEU* 3.5 2.2 + - + +
191B ASN* 3.6 19.5 - - + +
194B LYS* 3.2 34.8 + - + +
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Residues in contact with PRO 153 (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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72B TRP* 3.7 24.7 - - + -
76B PHE* 3.5 27.6 - - + -
125B TRP* 3.9 16.6 - - + -
126B LEU 4.0 4.7 - - - +
127B VAL* 4.2 5.6 - - + -
145B PRO* 3.9 21.5 - - + -
146B LEU* 4.2 17.7 - - + +
151B VAL 3.8 8.1 - - - +
152B THR* 1.4 90.0 - - + +
154B LEU* 1.3 59.5 + - - +
191B ASN* 3.6 13.5 - - - +
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Residues in contact with LEU 154 (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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76B PHE* 3.7 2.4 - - - -
80B CYS* 4.7 1.2 - - - -
126B LEU* 2.8 38.5 + - + +
127B VAL 3.9 16.8 - - - -
128B LYS* 3.8 13.2 - - + +
134B LEU* 4.0 8.5 - - + -
152B THR* 3.8 13.2 - - + +
153B PRO* 1.3 77.5 - - - +
155B LEU* 1.3 61.0 + - - +
188B VAL* 3.5 23.0 - - + +
191B ASN* 3.0 58.2 + - + +
192B LEU* 3.7 28.7 - - + +
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Residues in contact with LEU 155 (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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76B PHE* 3.8 7.5 - - - -
80B CYS* 3.9 17.3 - - + -
107B PHE* 4.2 24.7 - - + -
111B PHE* 4.3 9.2 - - + -
125B TRP* 3.3 6.8 - - - +
126B LEU* 2.9 37.4 + - + +
154B LEU* 1.3 81.1 - - + +
156B THR* 1.3 67.4 + - - +
179B PHE* 3.9 27.8 - - + -
180B TRP* 4.7 1.6 - - + -
183B VAL* 3.6 31.6 - - + -
185B TRP* 4.4 12.3 - - + -
188B VAL* 3.9 12.3 - - + -
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Residues in contact with THR 156 (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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73B ASN 4.6 0.9 - - - +
76B PHE* 3.7 19.3 - - + -
77B TYR* 3.8 26.3 - - + +
80B CYS* 3.6 10.4 - - - +
111B PHE* 4.5 0.9 - - - -
123B TRP* 3.5 29.5 - - + +
124B THR 3.2 12.2 + - - -
125B TRP* 3.3 33.3 - - + -
155B LEU* 1.3 73.4 - - - +
157B VAL* 1.3 65.3 + - - +
179B PHE* 3.2 21.3 - - - -
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Residues in contact with VAL 157 (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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77B TYR* 4.2 2.0 - - + -
111B PHE* 3.7 20.6 - - + -
115B ALA* 4.2 4.9 - - + -
123B TRP* 3.5 4.6 - - - -
124B THR* 3.0 41.8 + - - -
156B THR* 1.3 77.4 + - - +
158B ASP* 1.3 63.4 + - - +
159B LEU* 3.6 13.0 + - + +
175B TYR* 3.6 31.6 - - + +
176B MET* 4.0 7.0 - - - -
179B PHE* 3.6 33.2 - - + -
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Residues in contact with ASP 158 (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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27B HIS* 2.7 12.8 + - - -
74B HIS* 3.3 3.3 + - - -
77B TYR* 3.5 26.6 - - + -
123B TRP* 3.4 28.7 - - + -
157B VAL* 1.3 71.7 - - - +
159B LEU* 1.3 58.4 + - - +
160B TRP* 3.1 31.9 + - - +
163B ALA* 3.6 9.4 - - + +
175B TYR* 2.6 32.4 + - - -
1195B FE 1.9 31.7 - - - -
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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