Contacts of the strand formed by residues 135 - 140 (chain 1) in PDB entry 1K2I
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 135 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331 GLY 3.4 7.2 + - - -
1341 THR* 1.3 77.9 - - - +
1361 CYS* 1.3 74.4 + - - +
1371 VAL* 5.9 0.7 - - + -
1591 SER* 3.9 20.4 - - - +
1601 LEU* 3.6 10.5 - - - +
1611 PRO* 4.3 6.4 - - - +
2011 CYS* 5.2 2.1 - - - +
2021 LYS 5.5 1.6 + - - -
2071 TRP* 5.9 0.5 - - - -
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Residues in contact with CYS 136 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341 THR* 4.0 6.3 - - - -
1351 THR* 1.3 79.9 - - - +
1371 VAL* 1.3 67.7 + - - +
1591 SER* 3.2 7.4 - - - -
1601 LEU* 2.8 33.0 + - - +
1621 LEU* 3.8 23.3 - - + -
1991 LEU* 4.1 13.7 - - + -
2001 VAL 3.0 13.9 - - - +
2011 CYS* 2.0 46.2 - - - +
2071 TRP* 5.4 1.3 - - - -
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Residues in contact with VAL 137 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 LEU* 4.0 15.0 - - + -
271 TRP* 3.8 25.4 - - + -
1351 THR* 5.9 0.4 - - + -
1361 CYS* 1.3 81.4 - - - +
1381 THR* 1.3 72.9 + - - +
1391 THR* 4.2 5.4 - - + -
1571 GLN* 4.6 0.4 - - + -
1581 ALA 3.4 15.3 - - - +
1591 SER* 4.0 15.9 - - - +
1601 LEU* 4.1 0.2 - - - -
1981 PRO 3.9 0.2 - - - +
1991 LEU* 3.4 5.3 - - - -
2001 VAL* 2.8 51.8 + - + +
2071 TRP* 4.0 22.0 - - + -
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Residues in contact with THR 138 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 ILE* 3.4 16.0 - - + +
1371 VAL* 1.3 75.1 - - - +
1391 THR* 1.3 67.5 + - - +
1581 ALA* 3.0 41.5 + - + +
1601 LEU* 3.9 15.9 - - + +
1881 VAL* 6.2 0.2 - - + -
1901 SER* 3.8 19.5 + - - +
1941 ASP* 6.0 0.5 - - - +
1981 PRO 2.9 19.2 + - - -
1991 LEU* 4.2 11.9 - - - -
2131 VAL* 3.8 18.9 - - - +
2281 TYR* 4.1 3.0 - - - -
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Residues in contact with THR 139 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 ILE* 3.7 6.7 - - - -
271 TRP* 3.6 45.7 - - + +
291 TRP* 5.4 0.5 + - - -
301 GLN* 2.6 30.8 + - - +
1371 VAL* 4.2 4.3 - - + -
1381 THR* 1.3 85.4 + - - +
1401 GLY* 1.3 60.1 + - - +
1551 LEU* 4.4 6.3 - - - -
1561 GLN 3.2 13.9 - - - +
1571 GLN* 3.8 5.2 - - + -
1941 ASP* 4.3 5.2 - - - +
1971 GLY* 4.6 4.3 - - - -
1981 PRO* 3.5 23.5 + - - +
2001 VAL* 6.2 1.1 - - + -
2131 VAL* 5.1 0.9 - - - +
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Residues in contact with GLY 140 (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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161 ILE* 3.8 2.6 - - - +
301 GLN* 4.1 9.6 - - - -
1391 THR* 1.3 77.2 - - - +
1411 TRP* 1.3 58.8 + - - -
1421 GLY 3.8 0.5 + - - -
1551 LEU* 3.6 13.9 - - - +
1561 GLN* 3.1 37.4 + - - +
1931 GLY 5.6 0.2 - - - -
1941 ASP* 3.3 19.0 - - - +
1971 GLY* 6.2 0.2 - - - -
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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
------------------------------------------------------------
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