Contacts of the strand formed by residues 141 - 149 (chain B) in PDB entry 1LNU
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 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 3.1 10.1 - - - +
131B SER* 2.8 30.2 + - - -
132B ARG* 2.7 52.3 + - - +
140B ASN* 1.3 73.9 - - - +
142B LEU* 1.3 63.9 + - - +
143B VAL* 3.9 23.1 - - + -
187B MET* 4.1 13.9 - - + -
188B LEU 3.6 11.2 - - - +
189B GLU* 3.1 15.8 + - - +
190B MET* 3.8 2.2 - - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 5.2 1.3 - - + -
129B SER 3.3 10.8 - - - +
130B LEU* 3.5 17.7 - - + -
141B THR* 1.3 74.4 - - - +
143B VAL* 1.3 61.7 + - - +
158B TRP* 3.4 22.2 - - + -
187B MET 3.6 0.2 - - - -
188B LEU* 3.0 39.5 + - + +
190B MET* 3.3 39.5 - - + +
198B TYR* 3.8 34.8 - - + -
215B TRP* 4.1 31.6 - - + -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL 3.6 2.3 - - - +
128B ILE* 3.0 4.3 - - - -
129B SER* 2.7 45.5 + - - +
131B SER* 4.5 14.8 - - - +
141B THR* 3.9 9.6 - - + -
142B LEU* 1.3 73.5 - - - +
144B CYS* 1.3 65.8 + - - +
145B SER* 3.9 17.1 + - - +
158B TRP* 4.1 0.9 - - - -
185B LEU* 4.6 11.9 - - + -
186B VAL 3.8 7.0 - - - +
187B MET* 3.5 35.9 - - + -
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 5.1 6.3 - - - -
127B VAL 3.6 6.1 - - - -
128B ILE* 4.1 6.1 - - + +
143B VAL* 1.3 71.4 - - - +
145B SER* 1.3 63.2 + - - +
146B VAL* 3.8 15.5 + - - +
156B VAL* 4.7 0.7 - - - -
158B TRP* 3.2 19.9 - - + +
184B VAL 4.1 0.9 - - - +
186B VAL* 3.1 35.5 + - + +
200B CYS* 2.0 51.6 - - - -
202B VAL* 4.6 3.1 - - - -
213B VAL* 6.1 0.2 - - - -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PRO* 4.6 18.5 - - - +
125B ASN 3.1 12.1 - - - +
126B VAL* 3.2 15.8 - - - +
127B VAL* 3.0 23.0 + - - +
129B SER* 5.7 1.2 + - - -
143B VAL* 3.9 13.5 + - - +
144B CYS* 1.3 73.2 - - - +
146B VAL* 1.3 61.3 + - - +
147B THR* 3.8 12.0 + - - -
184B VAL 4.3 2.7 - - - -
185B LEU* 4.4 18.1 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.4 29.2 - - + -
125B ASN 3.2 4.0 - - - +
126B VAL* 4.2 1.8 - - + -
144B CYS* 4.2 12.8 - - - +
145B SER* 1.3 77.0 - - - +
147B THR* 1.3 61.0 + - - +
149B PHE* 3.2 4.2 - - + -
154B ILE* 3.5 21.1 - - + -
156B VAL* 3.6 25.1 - - + -
183B GLN* 3.2 3.1 - - - +
184B VAL* 2.9 45.5 + - + +
185B LEU* 4.8 0.2 - - - +
186B VAL* 5.0 0.2 - - + -
202B VAL* 3.8 19.7 - - + -
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Residues in contact with THR 147 (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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95A LYS 4.1 9.4 - - - +
96A SER* 4.9 2.2 - - - -
97A PRO* 4.2 23.2 - - + +
124B PRO* 3.3 4.7 - - - +
125B ASN* 3.0 50.0 + - - +
145B SER* 3.8 8.2 + - - -
146B VAL* 1.3 81.0 - - - +
148B ASP* 1.3 80.1 + - - +
149B PHE* 3.2 4.4 + - - -
182B PHE 3.6 0.7 - - - -
183B GLN* 3.8 26.7 - - + +
185B LEU* 5.1 2.2 - - + -
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Residues in contact with ASP 148 (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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95A LYS* 3.1 42.6 + - - +
96A SER* 4.5 10.9 - - - -
122B GLU* 3.9 12.0 - - - +
123B GLN 3.5 11.8 - - - +
125B ASN* 3.1 22.4 + - - +
147B THR* 1.3 82.2 + - - +
149B PHE* 1.3 59.3 + - - +
177B ASN* 4.9 1.6 + - - +
181B THR* 3.9 16.3 + - + +
182B PHE 3.1 8.9 + - - -
183B GLN* 4.3 1.8 - - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 3.3 13.5 - - - +
124B PRO* 3.6 20.9 - - + -
146B VAL* 3.2 24.0 - - + -
147B THR 3.8 4.9 - - - -
148B ASP* 1.3 75.4 - - - +
150B TYR* 1.3 64.7 + - - +
151B PRO 3.5 17.0 - - - -
152B ALA 4.2 4.5 - - - -
154B ILE* 3.9 22.0 - - + -
174B LEU* 4.8 2.5 - - - -
181B THR* 3.1 1.7 - - - -
182B PHE* 2.4 84.4 + + + +
183B GLN* 3.0 22.2 - - - -
184B VAL* 3.5 17.0 - - + -
205B PRO* 4.2 10.8 - - + -
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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