Contacts of the strand formed by residues 206 - 215 (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 ALA 206 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11 CYS 4.0 15.7 - - - +
21 GLY 3.6 9.9 - - - +
31 VAL* 4.3 6.1 - - + -
1221 CYS* 4.1 12.6 - - - -
2021 LYS* 4.2 2.9 - - - -
2031 LYS 2.8 33.2 + - - +
2041 ASN 3.3 2.6 - - - +
2051 GLY* 1.3 79.8 - - - +
2071 TRP* 1.3 63.9 + - - +
2081 THR* 3.4 4.9 + - - +
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Residues in contact with TRP 207 (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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21 GLY* 2.9 31.7 + - - +
41 PRO* 3.8 12.4 - - + +
81 PRO* 4.5 11.7 - - + +
101 LEU* 5.0 9.6 - - + -
271 TRP* 3.9 21.0 - + - -
291 TRP* 3.5 34.1 - + + -
1211 VAL* 3.6 2.5 - - - +
1221 CYS* 3.3 24.3 + - - +
1351 THR 5.9 0.7 - - - -
1361 CYS* 5.3 1.3 - - - -
1371 VAL* 4.0 22.7 - - + -
2001 VAL* 3.5 36.1 - - + -
2011 CYS* 3.7 5.6 - - - -
2021 LYS* 3.7 59.6 - - + +
2051 GLY 5.5 0.2 - - - -
2061 ALA* 1.3 70.3 - - - +
2081 THR* 1.3 58.5 + - - +
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Residues in contact with THR 208 (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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1221 CYS* 3.5 13.5 - - + +
1231 LEU 3.8 2.9 - - - +
1241 PRO* 3.5 42.6 - - + -
1281 ASP* 5.1 1.3 - - - +
1301 PHE* 4.2 15.9 - - + -
2001 VAL* 3.2 5.8 - - - -
2011 CYS 2.9 34.4 + - - -
2031 LYS* 3.8 12.7 + - - +
2061 ALA* 3.5 9.2 + - - +
2071 TRP* 1.3 75.9 + - - +
2091 LEU* 1.3 63.0 + - - +
2101 VAL* 3.2 6.6 + - - +
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Residues in contact with LEU 209 (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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451 SER* 4.0 6.1 - - - +
531 VAL* 3.7 30.5 - - + -
1211 VAL* 3.9 14.8 - - + +
1221 CYS 2.8 18.8 + - - +
1231 LEU* 4.1 18.8 - - + -
1241 PRO* 3.1 22.9 - - - +
1981 PRO* 3.4 34.3 - - + -
1991 LEU 3.9 3.4 - - - +
2001 VAL* 4.1 4.9 - - + -
2081 THR* 1.3 68.4 - - - +
2101 VAL* 1.3 59.7 + - - +
2111 GLY 3.5 18.2 - - - +
2121 ILE* 4.7 7.2 - - + -
2311 VAL* 3.4 20.3 - - + +
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Residues in contact with VAL 210 (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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1241 PRO* 5.2 1.8 - - - -
1301 PHE* 3.4 54.1 - - + -
1621 LEU* 4.7 3.4 - - + -
1811 ILE* 4.0 27.7 - - + +
1991 LEU* 3.0 11.9 + - + +
2011 CYS* 3.5 24.2 - - - -
2081 THR 3.2 9.6 + - - +
2091 LEU* 1.3 74.8 - - - +
2111 GLY* 1.3 59.0 + - - +
2291 ALA 3.7 0.9 - - - +
2301 ARG* 3.9 5.7 - - + +
2311 VAL* 3.1 24.2 + - - +
2321 THR* 4.7 3.9 + - + +
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Residues in contact with GLY 211 (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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1811 ILE* 4.6 0.9 - - - -
1981 PRO 3.8 0.2 - - - -
1991 LEU* 3.0 42.3 + - - +
2091 LEU* 3.5 12.2 - - - +
2101 VAL* 1.3 82.4 - - - +
2121 ILE* 1.3 64.8 + - - -
2281 TYR* 4.1 7.2 - - - -
2291 ALA 3.1 10.5 - - - -
2311 VAL* 3.9 2.0 - - - -
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Residues in contact with ILE 212 (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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531 VAL* 4.9 11.4 - - + -
541 THR 4.0 5.4 - - - +
551 ALA* 4.0 14.6 - - + +
1021 ASP 4.4 2.9 - - - +
1031 ILE* 3.7 41.3 - - + -
1961 GLY* 3.6 33.2 - - - +
1971 GLY 3.4 3.8 - - - +
2091 LEU* 4.7 8.5 - - + -
2111 GLY* 1.3 77.9 - - - +
2131 VAL* 1.3 71.3 + - - +
2141 SER* 3.0 2.1 + - - -
2281 TYR* 3.2 4.6 - - - +
2291 ALA* 2.8 37.9 + - + +
2311 VAL* 4.0 17.3 - - + -
2341 LEU* 5.2 0.7 - - + -
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Residues in contact with VAL 213 (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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551 ALA* 3.9 6.9 - - - +
1381 THR* 3.8 15.3 - - - +
1391 THR 5.1 1.6 - - - +
1901 SER* 3.9 13.9 - - - +
1941 ASP* 3.3 33.7 - - + +
1951 SER* 3.6 11.5 - - - +
1961 GLY* 2.9 23.2 + - - +
1971 GLY* 3.0 19.2 + - - +
1981 PRO 4.5 0.7 - - - +
2121 ILE* 1.3 69.2 - - - +
2141 SER* 1.3 59.4 + - - +
2271 VAL 5.3 0.2 - - - +
2281 TYR* 3.6 25.9 - - + -
4001 SN1 3.2 26.2 - - - +
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Residues in contact with SER 214 (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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571 HIS* 3.0 23.9 + - - -
991 ILE* 3.6 4.5 + - - +
1021 ASP* 2.7 35.1 + - - +
1801 MET* 6.5 0.4 - - - -
1951 SER* 3.8 5.0 + - - -
2121 ILE 3.0 8.8 + - - -
2131 VAL* 1.3 76.7 - - - +
2151 TRP* 1.3 80.4 + - - +
2271 VAL* 3.1 14.5 + - - -
2281 TYR* 4.1 1.1 - - - -
2291 ALA* 4.0 11.2 - - - -
4001 SN1 4.3 5.0 - - - +
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Residues in contact with TRP 215 (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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981 THR 5.1 1.6 - - - -
991 ILE* 3.8 34.2 - - + +
1721 TRP* 3.6 41.7 - + + -
1751 LYS* 3.7 52.3 - - + -
1761 ILE* 4.1 2.7 - - + -
1801 MET* 3.8 16.2 - - + +
2141 SER* 1.3 98.3 - - - +
2161 GLY* 1.3 82.4 + - - +
2261 GLY* 4.0 0.2 - - - -
2271 VAL* 2.7 63.7 + - + +
4001 SN1 3.7 19.5 + - - -
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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