Contacts of the strand formed by residues 130 - 138 (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 ALA 130 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801 SER 3.5 6.1 - - - -
851 ASP* 5.8 0.2 - - + -
861 THR* 4.2 12.3 - - + +
891 VAL* 5.4 4.0 - - + -
1211 CYS* 4.9 6.9 - - - -
1281 LEU* 3.9 22.4 - - + +
1291 MET* 1.4 73.7 - - - +
1311 GLY* 1.3 59.5 + - - +
1321 ILE* 3.9 24.9 - - + -
1481 VAL* 3.8 14.7 - - - +
1491 PRO 3.9 5.2 - - - +
1501 MET* 3.3 19.2 - - - +
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Residues in contact with GLY 131 (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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371 ILE* 4.7 5.9 - - - +
781 CYS 3.6 1.9 - - - +
801 SER* 2.9 45.3 + - - -
1301 ALA* 1.3 73.8 - - - +
1321 ILE* 1.4 59.2 + - - +
1481 VAL 3.8 8.3 - - - -
1491 PRO* 5.3 1.3 - - - -
1501 MET* 3.4 13.3 - - - +
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Residues in contact with ILE 132 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ILE* 5.6 0.2 - - - -
771 CYS* 3.9 18.4 - - + -
781 CYS 3.3 13.9 - - - +
791 ARG* 5.2 3.6 - - + -
861 THR* 5.0 10.1 - - + +
891 VAL* 4.7 8.5 - - + -
1171 PHE* 3.8 30.7 - - + -
1211 CYS* 5.7 1.1 - - - -
1301 ALA* 3.9 24.7 - - + -
1311 GLY* 1.4 78.1 - - - +
1331 ILE* 1.4 75.9 + - - +
1341 ILE* 3.8 13.2 - - + -
1471 SER* 3.6 2.4 - - - -
1481 VAL* 2.9 47.8 + - + +
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Residues in contact with ILE 133 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ILE* 3.8 34.7 - - + +
381 MET* 3.9 22.9 - - - +
391 ALA* 3.8 26.7 - - + +
481 LEU* 5.5 1.0 - - + +
771 CYS* 3.4 2.8 - - - -
781 CYS* 2.9 43.3 + - + +
1321 ILE* 1.4 78.8 - - - +
1341 ILE* 1.3 67.0 + - - +
1351 ALA* 4.1 2.3 + - + +
1451 VAL* 4.2 7.9 - - + -
1461 TYR 3.5 11.2 - - - +
1471 SER* 4.6 9.9 - - - +
1601 ALA* 4.4 9.2 - - + +
1611 ILE 4.6 2.0 - - - +
1621 GLY* 4.4 9.0 - - - +
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Residues in contact with ILE 134 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 ILE* 5.6 0.7 - - + -
751 ILE* 4.1 8.5 - - + -
761 PHE 3.6 13.5 - - - +
771 CYS* 4.4 4.0 - - + +
1091 LEU* 3.9 25.0 - - + +
1131 ALA* 4.5 7.9 - - + +
1141 ALA* 4.4 18.2 - - - -
1171 PHE* 3.5 38.6 - - + -
1321 ILE* 3.9 17.9 - - + -
1331 ILE* 1.3 73.9 - - - +
1351 ALA* 1.4 61.1 + - - +
1451 VAL* 3.5 1.6 - - - -
1461 TYR* 2.7 50.0 + - + +
1481 VAL* 4.2 15.0 - - + -
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Residues in contact with ALA 135 (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 11.0 - - + -
461 VAL* 3.8 30.1 - - + -
481 LEU* 4.0 23.0 - - + +
741 ARG 4.3 0.2 - - - +
751 ILE* 4.2 0.9 - - - -
761 PHE* 2.8 32.0 + - - +
1091 LEU* 4.1 4.5 - - - +
1331 ILE* 4.0 3.0 + - + -
1341 ILE* 1.4 74.8 - - - +
1361 GLY* 1.4 58.9 + - - +
1441 GLN 3.5 7.6 - - - +
1451 VAL* 4.9 0.7 - - - -
2131 ILE* 5.9 0.2 - - - -
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Residues in contact with GLY 136 (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* 3.8 8.5 - - - +
741 ARG 3.5 12.6 - - - -
751 ILE* 4.6 1.1 - - - -
1091 LEU* 3.8 20.0 - - - +
1351 ALA* 1.4 75.8 - - - +
1371 TRP* 1.3 59.9 - - - -
1431 GLY* 3.2 2.8 - - - -
1441 GLN* 3.0 36.4 + - - +
2131 ILE* 5.5 0.7 - - - -
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Residues in contact with TRP 137 (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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431 ASP 5.5 0.8 + - - -
441 GLY 3.2 28.0 + - - -
451 GLY* 3.7 11.4 - - - -
741 ARG* 3.4 50.6 + - - +
751 ILE* 5.8 0.2 - - - +
1091 LEU* 6.2 0.2 - - - -
1361 GLY* 1.3 74.6 - - - +
1381 ASP* 1.4 68.2 + - - +
1391 PRO* 3.6 40.1 - - + +
1421 GLY* 4.6 3.0 - - - -
1431 GLY* 3.9 16.0 - - - +
2131 ILE* 3.6 27.8 - - + +
2141 ALA 3.8 13.7 - - - -
2151 GLU* 3.6 37.4 + - + -
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Residues in contact with ASP 138 (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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741 ARG* 5.8 1.3 - - + +
1061 GLU* 5.2 1.8 - - - +
1071 PRO 5.1 2.2 - - - +
1081 PRO* 3.7 5.3 - - + +
1091 LEU* 3.5 21.5 + - - +
1371 TRP* 1.4 82.0 + - - +
1391 PRO* 1.3 66.9 - - + +
1401 GLN* 3.1 29.9 - - - +
1411 GLU* 2.8 31.4 + - - +
1421 GLY* 3.0 38.3 + - - +
1441 GLN* 3.2 24.2 + - - +
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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