Contacts of the strand formed by residues 268 - 275 (chain B) in PDB entry 2LDX
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 ARG 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASN* 3.9 22.8 + - - +
182A THR* 4.5 19.5 + - + +
183A SER* 4.5 4.5 - - - +
257B ASP* 3.8 25.4 + - - -
260B ARG* 2.6 61.4 - - - +
261B SER* 4.4 6.9 + - - +
266B LEU* 2.9 20.9 + - + +
267B LYS* 1.3 77.0 - - - +
269B VAL* 1.3 62.7 + - - +
270B HIS* 3.0 40.4 + - + +
293B VAL* 4.3 0.4 - - - -
294B LEU* 3.4 15.9 + - - +
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Residues in contact with VAL 269 (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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179A VAL* 5.1 5.8 - - + -
183A SER* 2.7 39.0 + - - +
205A VAL* 5.4 10.1 - - + +
187B TRP* 4.7 20.4 - - + -
267B LYS 3.7 3.6 + - - -
268B ARG* 1.3 79.0 - - - +
270B HIS* 1.3 70.2 + - - +
271B PRO* 4.7 1.0 - - - +
291B PRO* 4.0 7.0 - - + +
292B CYS* 3.0 37.2 - - - +
293B VAL* 3.6 20.0 - - + +
303B VAL* 4.5 13.7 - - + -
8C ILE* 5.8 0.2 - - + -
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Residues in contact with HIS 270 (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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163B ASN* 3.3 17.9 + - - -
187B TRP* 4.9 0.4 - - - -
257B ASP* 3.3 31.2 - - - -
258B LEU* 3.9 5.9 - - + +
261B SER* 3.8 10.2 - - - -
268B ARG* 3.0 51.8 + - + +
269B VAL* 1.3 80.0 + - - +
271B PRO* 1.3 68.7 - - + +
272B VAL* 3.5 11.0 + - + -
290B ILE 3.3 1.7 - - - +
291B PRO* 3.8 3.6 - - - -
292B CYS* 2.4 50.1 + - - +
294B LEU* 3.3 31.9 - - + -
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Residues in contact with PRO 271 (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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162B CYS* 4.7 2.2 - - + -
163B ASN* 3.2 43.2 + - - +
166B SER* 3.6 28.3 - - - +
187B TRP* 3.7 37.0 - - + +
188B VAL 4.9 2.0 - - - +
189B LEU* 5.1 0.9 - - + -
269B VAL 4.7 0.4 - - - +
270B HIS* 1.3 84.0 - - + +
272B VAL* 1.3 67.4 + - - +
289B SER* 4.5 11.4 - - - +
290B ILE 3.6 8.5 - - - +
291B PRO* 4.1 2.9 - - + -
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Residues in contact with VAL 272 (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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158B ILE* 3.8 20.9 - - + -
159B GLY 3.4 15.3 - - - +
160B SER 5.4 0.2 - - - +
161B GLY* 4.4 1.6 - - - -
163B ASN* 4.8 1.6 - - + -
258B LEU* 3.4 33.2 - - + -
270B HIS* 3.5 11.4 - - + +
271B PRO* 1.3 82.7 - - - +
273B THR* 1.3 61.2 + - - +
274B THR 4.0 0.5 + - - -
289B SER* 3.2 7.6 - - - -
290B ILE 2.9 27.1 + - - +
292B CYS* 3.1 33.1 - - + -
294B LEU* 4.0 9.0 - - + -
299B ILE* 4.6 1.8 - - + -
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Residues in contact with THR 273 (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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139B VAL* 4.5 0.8 + - + -
140B ASP* 2.8 40.8 - - - +
143B THR* 3.2 17.2 + - - +
158B ILE* 3.9 5.7 - - - +
159B GLY* 3.0 37.5 + - - -
161B GLY* 3.4 22.2 - - - +
272B VAL* 1.3 72.7 - - - +
274B THR* 1.3 72.2 + - - +
287B PHE 5.0 0.9 - - - -
288B LEU* 3.4 9.0 - - - -
289B SER* 3.6 11.2 - - - +
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Residues in contact with THR 274 (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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154B VAL* 3.1 29.2 - - + -
157B VAL 4.5 0.2 - - - +
158B ILE* 4.8 0.2 - - + -
272B VAL 4.4 1.0 + - - -
273B THR* 1.3 82.2 - - - +
275B LEU* 1.3 64.0 + - - +
276B VAL* 3.2 7.7 + - - +
287B PHE* 3.1 24.7 - - - -
288B LEU 2.8 18.0 + - - +
290B ILE* 4.7 7.3 - - - +
292B CYS* 3.9 18.4 - - - -
299B ILE* 3.7 30.3 - - + -
302B PHE* 4.7 13.1 - - - -
11C LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 275 (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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147B TRP* 4.2 18.2 - - + -
154B VAL* 4.4 13.9 - - + -
274B THR* 1.3 76.7 - - - +
276B VAL* 1.3 58.8 + - - +
277B LYS* 2.9 45.8 + - + +
279B PHE* 4.9 5.5 - - - -
285B GLU* 3.3 57.4 - - + +
286B VAL 3.8 2.5 - - - +
287B PHE* 3.4 21.7 - - + -
302B PHE* 5.2 10.9 - - - -
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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