Contacts of the strand formed by residues 137 - 144 (chain D) in PDB entry 1L9W
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.8 19.1 - - + -
5D THR 3.6 25.6 + - - -
6D VAL* 3.7 18.4 - - + -
111D ASP* 3.1 14.7 + - + -
112D MET* 3.0 23.4 - - + +
113D ILE 2.9 25.6 + - - -
132D HIS* 5.1 3.1 - + - -
135D ASN* 3.6 34.6 + - - -
136D VAL* 1.3 74.3 - - - +
138D VAL* 1.3 63.7 + - - +
167D ASP* 3.3 30.3 - - + +
168D ILE* 5.7 1.3 - - + -
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Residues in contact with VAL 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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113D ILE* 3.6 10.3 - - + +
115D LEU* 3.7 28.3 - - + -
128D VAL* 4.2 21.5 - - + -
131D ALA* 3.6 29.6 - - + -
132D HIS* 4.6 4.9 - - - +
136D VAL 4.3 1.8 - - - +
137D TYR* 1.3 80.4 - - - +
139D VAL* 1.3 73.6 + - - +
140D MET* 3.8 7.5 + - + +
166D ALA* 3.9 4.9 - - - -
167D ASP* 2.8 42.9 + - - +
168D ILE 3.1 6.9 + - - -
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Residues in contact with VAL 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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78D LEU* 4.0 28.3 - - + -
112D MET* 4.5 9.9 - - + -
113D ILE 3.0 10.8 + - - +
114D ASP* 3.2 16.2 - - - +
115D LEU 2.9 24.4 + - - -
138D VAL* 1.3 75.0 - - - +
140D MET* 1.3 62.0 + - - +
141D SER 3.9 0.2 + - - -
168D ILE* 3.4 34.5 - - + +
170D LYS* 3.9 31.4 - - + +
201D ILE* 5.0 8.5 - - + -
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Residues in contact with MET 140 (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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115D LEU* 3.2 17.7 - - + +
117D LEU* 4.1 13.9 - - - +
124D VAL* 4.0 17.3 - - + -
128D VAL* 3.9 20.9 - - + -
138D VAL* 3.8 4.5 + - + -
139D VAL* 1.3 73.6 - - - +
141D SER* 1.3 54.3 + - - +
161D MET* 3.3 37.9 - - + +
164D LEU* 3.8 20.2 - - + -
166D ALA* 3.3 42.8 - - + +
168D ILE 3.0 7.9 + - - +
169D PRO 3.5 0.3 - - - -
170D LYS* 2.8 31.4 + - - +
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Residues in contact with SER 141 (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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82D ARG* 3.3 11.5 + - - -
86D GLU* 4.1 0.5 - - - +
114D ASP* 2.7 36.3 + - - -
115D LEU 3.0 4.2 + - - -
116D GLU* 3.3 10.2 - - - +
117D LEU 3.0 23.9 + - - -
140D MET* 1.3 74.7 - - - +
142D ASN* 1.3 61.7 - - - +
143D HIS* 3.4 15.8 - - - -
161D MET* 3.4 3.8 - - - -
170D LYS* 3.3 17.9 - - - -
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Residues in contact with ASN 142 (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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86D GLU* 3.5 11.0 + - - -
117D LEU* 4.4 5.6 - - + +
118D PHE* 3.5 36.9 - - - -
141D SER* 1.3 77.1 - - - +
143D HIS* 1.3 74.0 + - - +
157D ARG* 2.8 40.1 + - - +
161D MET* 3.6 15.5 - - + -
170D LYS 3.1 5.3 + - - +
171D ILE* 3.2 17.1 - - + +
172D ALA 2.9 24.6 + - - -
173D VAL* 5.9 0.3 - - - +
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Residues in contact with HIS 143 (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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82D ARG* 3.2 37.9 + - - -
85D LYS 5.4 0.9 - - - +
86D GLU* 2.6 57.9 + - + +
141D SER* 3.4 25.0 - - - -
142D ASN* 1.3 85.4 + - - +
144D ASP* 1.3 61.2 + - - +
145D PHE* 3.8 19.7 + + + -
157D ARG* 5.3 0.5 + - - -
170D LYS* 4.9 3.4 + - - +
172D ALA* 3.3 28.6 + - + +
173D VAL* 5.5 0.2 - - - -
205D MET* 5.7 0.2 - - - -
304D DHS 3.4 20.4 - - + +
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Residues in contact with ASP 144 (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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143D HIS* 1.3 73.0 - - - +
145D PHE* 1.3 60.0 + - - +
146D HIS* 3.0 13.7 + - - +
147D GLN* 3.0 59.9 + - - +
149D PRO* 4.3 7.9 - - + +
157D ARG* 4.7 11.9 + - - +
172D ALA 3.0 8.1 + - - -
173D VAL* 3.5 12.4 - - + +
174D MET 3.1 25.1 + - - -
205D MET* 3.4 5.7 - - - +
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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