Contacts of the strand formed by residues 168 - 179 (chain A) in PDB entry 2W2R
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 LYS 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER* 3.5 1.4 - - - -
75A ASN* 3.0 48.1 + - + +
162A PHE* 3.3 22.2 - - - +
163A ASN* 3.8 29.3 - - + +
165A GLY 4.3 12.5 + - - -
167A TYR* 1.3 75.2 - - - +
169A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 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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73A ARG* 3.1 11.7 - - - -
74A SER 5.1 0.4 - - - -
161A PRO* 3.3 4.7 - - - +
162A PHE* 2.9 33.4 + - - +
168A LYS* 1.3 76.9 - - - +
170A THR* 1.3 69.2 + - - +
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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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71A THR 4.0 0.3 - - - +
72A VAL* 3.5 3.3 - - - -
73A ARG* 2.9 73.1 + - - +
160A LYS 3.4 10.5 - - - +
161A PRO* 4.4 6.5 - - + -
162A PHE* 3.5 1.0 - - - -
169A GLY* 1.3 80.5 - - - +
171A LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 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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71A THR 3.5 2.7 - - - -
72A VAL* 3.9 24.9 - - + -
73A ARG* 4.8 1.2 + - - -
87A ALA 3.4 25.8 - - - +
88A VAL* 3.7 5.8 - - - +
90A GLN 4.1 3.1 - - - -
91A TRP* 3.6 32.3 - - + +
158A PHE 4.2 1.6 - - - +
159A ARG* 3.3 5.4 - - - +
160A LYS* 2.8 44.3 + - + +
161A PRO 4.6 1.8 - - - +
162A PHE* 3.5 30.3 - - + -
170A THR* 1.3 81.2 - - - +
172A ASP* 1.3 60.9 + - - +
173A PHE* 3.9 17.3 - - + -
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Residues in contact with ASP 172 (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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69A LYS 3.8 2.1 - - - +
70A MSE 3.7 1.6 - - - -
71A THR* 2.9 41.0 + - - -
73A ARG* 3.6 30.4 + - - +
157A THR* 3.9 10.9 - - - +
158A PHE 3.4 2.9 - - - -
159A ARG* 3.8 30.7 + - + +
171A LEU* 1.3 75.1 - - - +
173A PHE* 1.3 63.9 + - - +
174A THR* 4.6 2.6 + - - -
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Residues in contact with PHE 173 (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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69A LYS 3.3 3.1 - - - +
70A MSE 3.6 37.0 - - + -
71A THR 3.6 17.5 - - - -
72A VAL* 4.0 5.2 - - + -
88A VAL* 3.9 23.8 - - + -
91A TRP* 3.5 35.0 - + + -
156A GLU 3.9 0.7 - - - +
157A THR* 3.2 4.0 - - - +
158A PHE* 2.8 44.5 + - + +
171A LEU* 3.9 25.4 - - + -
172A ASP* 1.3 83.5 + - - +
174A THR* 1.3 62.2 + - - +
175A PHE* 3.6 34.3 - + + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A MSE 3.9 0.7 - - - +
68A LEU* 3.4 5.0 - - - -
69A LYS* 2.8 52.5 + - + +
155A SER* 4.0 22.0 - - - +
156A GLU 3.4 5.4 - - - +
157A THR* 2.9 28.9 + - - +
172A ASP* 4.6 3.1 + - - -
173A PHE* 1.3 73.8 + - - +
175A PHE* 1.3 65.7 + - - +
176A THR* 5.0 1.1 - - - +
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Residues in contact with PHE 175 (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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67A MSE 3.5 2.5 - - - -
68A LEU* 3.8 8.1 - - + -
70A MSE 3.9 27.4 - - + -
91A TRP* 4.2 15.0 - + - -
105A TYR* 3.5 51.8 + + + -
108A ILE* 3.6 24.0 - - + -
109A ALA* 3.8 17.9 - - + -
155A SER* 3.3 2.0 - - - -
156A GLU* 2.9 33.6 + - - +
158A PHE* 4.0 13.7 - + - -
173A PHE* 3.6 34.5 - + + -
174A THR* 1.3 80.3 - - - +
176A THR* 1.3 61.9 - - - +
177A VAL 4.3 0.2 - - - -
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Residues in contact with THR 176 (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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66A PHE* 3.0 6.7 - - - +
67A MSE 2.8 60.8 + - + +
105A TYR* 4.9 0.2 - - - -
153A ASN* 3.5 27.8 - - - +
154A VAL 4.0 22.7 - - - +
155A SER* 3.1 22.1 - - - +
174A THR* 5.0 1.9 - - - +
175A PHE* 1.3 71.9 - - - +
177A VAL* 1.3 69.8 + - - +
178A SER* 5.2 0.9 - - - +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.8 21.3 - - + -
65A ARG 3.3 2.7 - - - -
66A PHE* 4.2 6.7 - - + -
101A LYS* 3.1 32.4 + - + +
104A PHE* 3.9 26.0 - - + +
105A TYR* 3.9 24.0 - - + -
108A ILE* 3.8 22.0 - - + -
151A MSE 3.9 21.8 - - + -
152A PHE 3.3 2.6 - - - +
154A VAL 5.0 0.2 + - - -
175A PHE 4.3 0.4 - - - -
176A THR* 1.3 82.6 - - - +
178A SER* 1.3 64.6 - - - +
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Residues in contact with SER 178 (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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64A PHE* 3.4 7.0 - - - +
65A ARG* 2.6 71.8 + - - +
151A MSE 3.4 17.9 - - - -
152A PHE* 3.6 16.6 - - - -
153A ASN* 3.7 10.9 + - - +
176A THR* 5.2 0.9 - - - +
177A VAL* 1.3 76.9 - - - +
179A ASP* 1.3 62.2 + - - +
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Residues in contact with ASP 179 (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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62A GLU* 5.9 1.4 - - - +
63A LYS 4.0 7.6 - - - +
64A PHE* 4.6 0.4 - - - +
65A ARG* 2.9 24.8 + - - -
148A ILE* 5.9 0.3 - - - +
149A PRO 4.7 0.3 - - - +
150A PRO* 3.1 31.5 - - - +
151A MSE 2.9 44.6 + - - +
152A PHE* 5.5 0.2 - - - -
178A SER* 1.3 72.4 - - - +
180A ASP* 1.3 63.1 + - - +
181A GLU* 3.9 5.3 + - + +
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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