Contacts of the strand formed by residues 132 - 139 (chain D) in PDB entry 3LSU
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 GLY 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D VAL* 3.6 8.0 - - - +
130D GLY 4.0 0.2 + - - -
131D SER* 1.3 77.0 - - - +
133D TRP* 1.3 62.0 + - - -
151D THR 3.2 11.4 - - - -
153D ASN 3.7 14.4 - - - -
169D ALA* 2.8 36.3 + - - -
170D TRP* 3.5 13.9 + - - +
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Residues in contact with TRP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.4 51.5 - - + +
81D HIS* 3.8 20.4 - + - -
84D PHE* 3.9 17.9 - + + -
125D LEU* 4.6 0.9 - - - -
128D VAL* 4.0 10.2 - - - +
132D GLY* 1.3 77.5 - - - -
134D ALA* 1.3 60.4 + - - +
135D PHE* 3.4 24.2 - + + -
150D GLN* 3.3 4.5 - - - -
151D THR* 2.9 34.5 + - - +
153D ASN 3.4 15.9 + - - -
154D GLN* 2.9 19.6 + - - -
155D ASP 4.4 0.2 - - - -
166D ALA* 4.0 11.0 - - + -
167D ILE 3.3 27.4 - - - -
168D ASP* 3.4 42.6 - - + -
169D ALA 4.4 0.7 - - - +
170D TRP* 3.9 4.6 - - - +
208D MN 4.4 0.2 - - - -
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D THR* 4.3 15.5 - - + -
124D MLY 4.5 8.7 - - + -
125D LEU* 3.5 39.2 - - + +
133D TRP* 1.3 73.8 - - - +
135D PHE* 1.3 64.0 + - - +
136D ILE 4.3 0.2 - - - -
148D VAL* 4.7 1.6 - - + -
149D VAL 3.3 9.4 - - - +
150D GLN* 5.0 0.9 - - - -
165D VAL 3.8 0.5 - - - +
166D ALA* 3.7 1.7 - - - -
167D ILE* 2.9 34.8 + - + +
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.3 30.5 - - - -
83D LEU* 4.4 8.1 - - + -
121D THR* 5.8 0.2 - - - -
133D TRP* 3.4 19.5 - + + -
134D ALA* 1.3 75.6 - - - +
136D ILE* 1.3 62.6 + - - +
137D VAL* 3.6 19.7 + - + -
148D VAL* 3.3 5.4 - - - +
149D VAL* 2.8 38.8 + - + +
151D THR* 3.4 34.3 - - + -
155D ASP 4.4 0.7 - - - -
156D THR* 3.8 9.6 - - - -
157D VAL* 3.8 18.6 - - + -
163D PRO* 4.0 15.9 - - + -
165D VAL 3.2 4.7 - - - +
166D ALA* 3.5 32.1 - - + -
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 6.1 1.3 - - + -
117D LEU* 3.9 25.1 - - + -
121D THR* 3.8 29.6 - - + +
134D ALA 4.3 0.2 - - - -
135D PHE* 1.3 73.1 - - - +
137D VAL* 1.3 63.4 + - - +
146D LEU* 4.9 7.6 - - + -
147D ASP 3.4 10.3 - - - +
148D VAL* 4.4 4.5 - - + +
163D PRO* 3.8 0.5 - - - +
164D LEU* 2.8 41.0 + - + +
165D VAL* 2.9 26.3 + - + +
167D ILE* 6.4 0.2 - - + -
190D TRP* 4.0 14.1 - - + -
195D TRP* 3.6 32.3 - - + -
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Residues in contact with VAL 137 (chain D).
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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135D PHE* 3.6 24.7 - - + +
136D ILE* 1.3 79.1 - - - +
138D MLY 1.3 63.7 + - - +
139D ASN* 4.7 0.7 - - + +
146D LEU* 3.2 10.6 - - - +
147D ASP* 2.8 54.7 + - + +
149D VAL* 3.9 17.9 - - + -
157D VAL* 4.1 17.0 - - + -
161D LEU* 4.2 21.5 - - + -
162D VAL 3.2 15.5 - - - +
163D PRO* 4.2 0.9 - - + -
164D LEU* 3.7 5.4 - - - -
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Residues in contact with MLY 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA* 6.0 0.4 - - - -
137D VAL* 1.3 74.8 - - - -
139D ASN* 1.3 59.5 + - - +
140D LEU* 3.5 18.4 + - + -
144D GLY* 3.5 37.5 - - - +
145D MLY 3.6 3.8 - - - -
146D LEU* 4.5 0.2 - - - -
160D PRO 3.2 4.2 - - - +
161D LEU* 3.8 0.2 - - - -
162D VAL* 2.9 36.0 + - + +
164D LEU* 3.7 20.7 - - + +
201D ARG 5.5 0.2 - - - +
202D PHE* 2.9 63.1 + - + +
203D ASP* 4.3 11.0 - - - -
204D ALA 4.9 0.4 - - - -
205D GLY* 4.1 18.8 - - - -
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B MLY 5.3 3.0 - - - -
147B ASP* 3.1 38.6 + - - -
137D VAL* 4.0 3.0 - - + +
138D MLY 1.3 71.4 - - - +
140D LEU* 1.3 59.0 + - - +
141D SER* 2.8 26.0 + - - -
142D ASN* 2.8 38.8 - - - +
144D GLY* 2.9 17.9 + - - -
145D MLY 2.8 15.8 + - - +
147D ASP* 5.6 4.0 - - + +
160D PRO* 3.6 8.8 - - - +
161D LEU* 3.7 23.6 - - + +
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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