Contacts of the strand formed by residues 225 - 230 (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 PRO 225 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1631 LEU* 3.5 25.6 - - + -
1681 CYS* 4.0 8.3 - - - -
1711 TYR* 3.4 39.9 - - + -
1721 TRP* 3.1 35.1 + - - +
1821 CYS* 4.2 4.9 - - + -
1831 ALA 3.7 8.5 - - - +
1851 ALA* 3.9 11.4 - - + +
2161 GLY* 4.7 1.0 - - - -
2171 SER 5.0 0.5 + - - -
2241 THR* 1.3 95.6 - - + +
2261 GLY* 1.3 65.3 + - - +
2271 VAL* 4.1 0.3 + - - +
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Residues in contact with GLY 226 (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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1821 CYS* 3.3 6.6 - - - +
1831 ALA 2.8 35.4 + - - -
1841 GLY* 4.7 0.4 - - - -
1891 SER* 5.7 4.0 + - - -
1901 SER* 6.0 3.6 - - - -
2151 TRP 4.0 5.6 - - - -
2161 GLY* 4.8 3.8 - - - -
2241 THR 3.7 2.0 + - - -
2251 PRO* 1.3 75.4 - - - +
2271 VAL* 1.3 60.4 + - - -
2281 TYR* 3.5 14.2 - - - -
4001 SN1 5.2 7.0 - - - -
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Residues in contact with VAL 227 (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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1721 TRP* 3.9 22.4 - - + +
1761 ILE* 4.0 8.1 - - + -
1801 MET* 3.8 29.4 - - + -
1811 ILE 3.8 4.0 - - - +
1821 CYS* 4.4 4.0 - - - +
2131 VAL* 5.3 0.2 - - - +
2141 SER* 3.1 7.1 + - - -
2151 TRP* 2.7 91.9 + - + +
2251 PRO 4.4 0.4 - - - +
2261 GLY* 1.3 75.4 - - - +
2281 TYR* 1.3 68.7 - - - +
4001 SN1 5.1 0.9 + - - -
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Residues in contact with TYR 228 (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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1381 THR* 4.1 4.9 - - - +
1601 LEU* 3.6 22.0 - - + +
1801 MET* 3.3 6.0 - - - +
1811 ILE* 2.8 49.4 + - + +
1831 ALA* 3.9 18.6 + - + -
1901 SER* 2.8 27.0 + - - -
1991 LEU* 3.7 31.6 - - + -
2111 GLY* 4.1 2.5 - - - -
2121 ILE 3.2 13.9 - - - +
2131 VAL* 3.6 41.1 - - + -
2141 SER* 4.1 2.9 - - - -
2261 GLY* 3.5 27.7 - - - -
2271 VAL* 1.3 76.8 - - - +
2291 ALA* 1.3 60.3 + - - +
4001 SN1 5.8 0.4 - - - -
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Residues in contact with ALA 229 (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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1021 ASP* 3.7 35.4 - - + +
1791 ALA 3.7 7.2 - - - +
1801 MET* 4.6 2.2 - - - +
1811 ILE* 4.4 0.4 - - - -
2111 GLY* 3.1 24.8 - - - -
2121 ILE* 2.8 24.9 + - + +
2141 SER* 4.0 4.1 - - - -
2281 TYR* 1.3 69.8 - - - +
2301 ARG* 1.3 59.2 + - - +
2311 VAL* 3.2 4.5 + - - +
2341 LEU* 4.0 17.3 - - + -
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Residues in contact with ARG 230 (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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1301 PHE 5.6 2.4 + - - -
1631 LEU 5.4 1.2 + - - -
1641 SER* 6.1 0.2 - - - +
1651 ASN* 2.7 36.4 + - - +
1781 ASP 3.3 16.5 + - - -
1791 ALA* 2.9 23.1 + - - +
1801 MET 3.0 21.7 + - - +
1811 ILE* 3.6 35.4 - - + +
2101 VAL* 3.9 6.1 - - + +
2281 TYR 3.3 1.8 + - - -
2291 ALA* 1.3 67.9 - - - +
2311 VAL* 1.3 63.7 + - - +
2321 THR* 3.4 23.1 + - - +
2331 ALA* 3.1 18.4 + - + +
2341 LEU* 3.5 15.4 - - - +
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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