Contacts of the strand formed by residues 142 - 148 (chain 1) in PDB entry 5LN3
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 142 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1371 TRP* 4.3 5.4 - - - -
1381 ASP* 3.0 28.8 + - - +
1391 PRO* 4.1 3.5 - - - -
1401 GLN 3.7 0.8 - - - +
1411 GLU* 1.3 81.2 - - - +
1431 GLY* 1.3 58.8 + - - -
1441 GLN* 3.1 20.8 + - - +
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Residues in contact with GLY 143 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411 GLN* 4.6 14.5 + - - +
451 GLY* 4.9 12.8 - - - -
461 VAL* 5.2 1.1 - - - -
1361 GLY 3.2 13.9 - - - -
1371 TRP* 3.9 15.8 - - - -
1411 GLU 4.5 1.4 - - - +
1421 GLY* 1.3 75.2 - - - -
1441 GLN* 1.4 58.1 + - - +
1451 VAL* 5.7 0.2 - - - -
1561 ARG* 3.4 23.5 + - - -
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Residues in contact with GLN 144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461 VAL* 4.4 3.1 - - - +
1091 LEU* 3.4 28.5 - - + +
1101 VAL* 4.3 17.2 - - + +
1351 ALA* 3.5 4.8 - - - +
1361 GLY 3.0 32.7 + - - +
1381 ASP* 3.2 26.4 + - - +
1411 GLU* 3.7 20.0 - - + +
1421 GLY 3.1 21.6 + - - +
1431 GLY* 1.4 74.8 - - - +
1451 VAL* 1.3 68.0 + - - +
1461 TYR* 4.0 14.4 - - + -
1561 ARG* 3.6 24.7 - - - +
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Residues in contact with VAL 145 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 ALA* 4.2 20.9 - - + +
411 GLN* 4.5 22.7 - - + +
461 VAL* 4.7 12.8 - - + -
1331 ILE* 4.2 12.1 - - + -
1341 ILE 3.5 4.0 - - - +
1351 ALA* 4.5 0.4 - - - +
1441 GLN* 1.3 83.8 - - - +
1461 TYR* 1.3 73.8 + - - +
1551 VAL 3.4 0.2 - - - +
1561 ARG* 3.6 3.6 - - - +
1571 GLN* 3.1 42.8 + - + +
1581 SER 4.6 2.2 - - - +
1591 PHE* 4.6 3.8 - - - -
1601 ALA* 4.2 21.8 - - + +
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Residues in contact with TYR 146 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 LEU* 3.8 19.7 - - + -
1101 VAL* 3.6 36.0 - - + +
1111 HIS* 5.5 0.5 + - - -
1141 ALA* 4.4 17.5 - - + -
1331 ILE* 3.5 5.9 - - - +
1341 ILE* 2.7 48.2 + - + +
1441 GLN* 4.0 8.7 - - + -
1451 VAL* 1.3 87.9 - - - +
1471 SER* 1.4 62.9 + - - +
1481 VAL 4.2 0.2 - - - -
1541 MET* 4.1 13.2 - - + -
1551 VAL* 3.3 26.9 - - - -
1561 ARG* 3.5 42.5 - - - +
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Residues in contact with SER 147 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321 ILE 3.6 6.3 - - - -
1331 ILE* 4.6 7.1 - - - +
1451 VAL* 4.9 1.0 - - - +
1461 TYR* 1.4 76.2 + - - +
1481 VAL* 1.4 59.2 + - - +
1491 PRO* 3.3 5.2 - - - +
1531 MET 2.8 24.9 - - - +
1541 MET* 4.3 0.8 - - - -
1551 VAL* 3.6 13.3 + - - +
1571 GLN* 4.7 6.2 - - - +
1601 ALA* 3.7 25.8 - - - +
807 ARG* 6.4 1.6 - - - -
817 PHE* 4.8 15.9 - - - -
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Residues in contact with VAL 148 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141 ALA 5.8 1.1 - - - +
1171 PHE* 4.5 12.1 - - + -
1181 LYS* 5.9 1.6 - - - +
1211 CYS* 3.9 25.4 - - - -
1301 ALA 3.8 13.2 - - - +
1311 GLY* 3.8 4.9 - - - -
1321 ILE* 2.9 48.9 + - + +
1341 ILE* 4.2 22.7 - - + -
1461 TYR* 5.5 0.4 - - + -
1471 SER* 1.4 74.4 - - - +
1491 PRO* 1.4 73.8 - - - +
1521 GLY* 4.5 5.2 - - - -
1531 MET 3.8 4.3 - - - +
1541 MET* 6.3 2.9 - - + -
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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