Contacts of the strand formed by residues 295 - 302 (chain A) in PDB entry 1LAN
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 ASN 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A TYR 3.3 2.7 - - - -
235A LYS* 3.4 11.4 - - - +
236A GLY 3.4 7.3 + - - -
237A SER* 3.1 27.9 + - - +
239A ASN 3.4 20.4 + - - -
240A ALA* 3.5 14.4 + - - +
242A GLU* 2.9 28.5 + - + +
243A PRO 4.6 2.5 + - - +
244A PRO* 3.3 7.4 - - + +
245A LEU* 3.0 26.4 + - - +
294A ILE* 1.3 74.6 - - - +
296A ILE* 1.3 63.3 + - - +
503A MRD 3.7 21.0 + - + +
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Residues in contact with ILE 296 (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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232A ILE 3.9 0.3 - - - +
233A HIS* 3.6 1.0 - - - -
234A TYR* 2.8 61.5 + - + +
245A LEU* 3.4 13.9 - - + +
247A PHE* 4.3 15.5 - - + -
284A ILE* 4.0 27.8 - - + +
287A ALA* 3.9 24.0 - - + -
294A ILE* 4.1 24.5 - - + +
295A ASN* 1.3 80.4 - - - +
297A VAL* 1.3 69.8 + - - +
479A LEU* 4.2 11.4 - - + -
503A MRD 3.4 5.1 - - - +
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Residues in contact with VAL 297 (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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232A ILE 3.3 8.7 - - - +
233A HIS* 4.2 8.3 - - + -
244A PRO* 3.9 12.6 - - + -
245A LEU 2.9 7.4 + - - +
246A VAL* 3.4 14.2 - - + -
247A PHE* 2.8 27.9 + - - +
284A ILE* 4.2 2.9 - - - -
296A ILE* 1.3 80.2 - - - +
298A GLY* 1.3 60.8 + - - +
299A LEU* 3.8 27.6 - - + -
349A PHE* 4.0 24.5 - - + -
503A MRD 3.6 35.4 - - + +
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Residues in contact with GLY 298 (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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230A LEU* 3.6 1.6 - - - +
231A GLU* 3.4 5.2 - - - -
232A ILE* 2.9 45.1 + - - +
247A PHE 3.3 5.4 - - - -
280A ILE* 4.4 4.3 - - - -
281A CYS* 6.0 0.9 - - - -
284A ILE* 3.5 19.7 - - - +
297A VAL* 1.3 73.4 - - - +
299A LEU* 1.3 64.1 + - - +
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Residues in contact with LEU 299 (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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229A PHE* 4.0 14.4 - - + -
230A LEU 3.3 2.0 - - - -
231A GLU* 3.8 24.2 - - + -
246A VAL* 4.0 6.5 - - + -
247A PHE 2.8 13.4 + - - +
248A VAL* 3.2 11.9 - - + +
249A GLY 2.9 25.1 + - - -
280A ILE* 4.0 3.3 - - - +
297A VAL* 3.8 14.1 - - + -
298A GLY* 1.3 83.1 - - - +
300A ALA* 1.3 60.1 + - - +
301A PRO* 4.2 2.0 - - - -
342A ALA 3.9 6.3 - - - +
345A TYR* 3.9 28.0 - - + -
346A ALA* 3.7 36.8 - - + +
349A PHE* 4.0 5.4 - - + -
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Residues in contact with ALA 300 (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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229A PHE* 4.5 1.9 - - - -
230A LEU* 2.8 52.4 + - + +
249A GLY 3.5 10.1 - - - +
277A ALA* 3.9 22.9 - - + -
280A ILE* 5.0 0.4 - - + -
281A CYS* 4.6 7.4 - - - -
299A LEU* 1.3 75.6 - - - +
301A PRO* 1.3 70.4 - - - +
302A LEU* 3.4 11.1 + - + +
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Residues in contact with PRO 301 (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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216A PHE* 3.6 39.3 - - + -
228A VAL 3.9 1.6 - - - +
229A PHE* 3.9 12.8 - - + -
248A VAL* 4.7 0.2 - - + -
249A GLY 3.4 13.9 - - - +
251A GLY* 3.0 26.3 + - - +
299A LEU 4.2 1.3 - - - +
300A ALA* 1.3 84.0 - - - +
302A LEU* 1.3 58.7 + - - +
338A ILE* 3.8 34.8 - - + +
339A LEU* 5.1 1.6 - - + -
342A ALA* 3.8 21.5 - - + -
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Residues in contact with LEU 302 (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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180A PRO* 3.7 18.9 - - + +
183A PHE* 3.6 44.2 - - + -
184A ALA* 4.7 1.1 - - + -
216A PHE* 3.4 5.1 - - - -
227A PRO* 3.3 2.1 - - - +
228A VAL* 2.9 54.0 + - + +
230A LEU* 3.8 14.4 - - + -
251A GLY* 3.1 26.9 - - - +
253A THR* 4.2 12.1 - - + -
274A MET* 4.8 1.3 - - + -
277A ALA* 4.5 2.7 - - + -
300A ALA* 3.5 17.7 - - + +
301A PRO* 1.3 76.4 - - - +
303A CYS* 1.3 64.9 + - - +
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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