Contacts of the helix formed by residues 21 - 29 (chain D) in PDB entry 1KLG
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 MET 21 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 4.1 22.2 - - - +
17D PHE* 3.5 31.6 - - + -
19D GLY 3.8 1.4 + - - -
20D THR* 1.3 70.5 - - - +
22D GLY* 1.3 56.7 + - - +
23D ASN 3.1 0.2 - - - -
24D MET* 2.8 30.4 + - - +
25D LYS* 2.9 10.7 + - - +
174D TYR* 3.9 24.9 - - + -
175D GLU 3.3 15.0 - - - +
176D PHE 3.3 3.0 + - - -
178D SER* 3.0 51.0 - - - +
179D SER* 4.1 6.1 - - - +
201D MET* 4.7 1.1 - - - -
202D PRO* 4.0 21.1 - - + -
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 2.9 7.2 - - - +
21D MET* 1.3 75.3 - - - +
23D ASN* 1.3 58.4 + - - +
25D LYS* 3.5 9.0 - - - +
26D TYR* 2.8 29.8 + - - +
175D GLU 3.7 5.8 - - - -
176D PHE* 2.6 31.5 + - - -
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 2.9 38.5 + - - +
22D GLY* 1.3 78.4 - - - +
24D MET* 1.3 58.5 + - - +
26D TYR* 3.8 5.9 - - - +
27D LEU* 3.7 5.0 - - - +
208D PHE* 3.4 30.8 + - + +
210D GLN* 3.0 34.4 + - + +
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Residues in contact with MET 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 6.2 0.4 - - + -
20D THR 4.2 0.2 + - - -
21D MET* 2.8 23.3 + - - +
23D ASN* 1.3 75.7 - - - +
25D LYS* 1.3 67.8 + - - +
26D TYR 3.1 1.3 - - - -
27D LEU* 3.1 18.6 + - - +
28D TYR* 3.6 29.8 - - - -
164D ARG* 4.2 0.7 - - - -
174D TYR* 3.6 26.7 - - + -
200D MET 3.5 16.4 - - - +
202D PRO* 3.7 16.2 - - + -
208D PHE* 3.6 38.0 - - + -
213D TYR* 3.4 31.6 - - + -
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D MET 2.9 9.2 + - - +
22D GLY* 3.5 11.9 - - - +
24D MET* 1.3 78.1 - - - +
26D TYR* 1.3 63.0 + - - +
28D TYR 2.9 14.2 + - - -
29D ASP* 2.9 44.6 + - + +
168D ILE* 3.8 20.1 - - + +
174D TYR* 3.6 44.7 + - + +
175D GLU* 4.5 10.4 - - - +
176D PHE* 4.8 2.9 - - - +
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Residues in contact with TYR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLY 2.8 17.9 + - - +
23D ASN* 3.8 9.6 - - - +
25D LYS* 1.3 78.1 - - - +
27D LEU* 1.3 63.1 + - + +
28D TYR 3.4 0.2 + - - -
29D ASP* 3.9 6.2 + - - +
31D HIS* 3.1 55.8 - + - +
88D ASN 4.8 1.3 - - - -
89D TYR* 5.4 1.8 - - - -
90D TYR* 3.2 35.9 - + - -
210D GLN* 3.5 24.2 - - - -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASN 3.7 9.2 - - - +
24D MET* 3.1 9.9 + - - +
25D LYS 3.0 0.4 + - - -
26D TYR* 1.3 83.0 - - + +
28D TYR* 1.3 71.9 + - + +
31D HIS* 3.4 15.6 - - - +
87D SER* 2.7 26.2 + - - +
88D ASN 3.8 21.1 - - - +
89D TYR* 4.8 0.9 - - + -
161D ILE* 5.0 0.2 - - - +
208D PHE* 3.7 33.0 - - + -
210D GLN* 3.8 24.0 - - + +
213D TYR* 4.4 4.5 - - + -
214D LEU* 3.9 33.7 - - + -
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D MET* 3.6 26.5 - - - -
25D LYS 2.9 3.0 + - - -
27D LEU* 1.3 94.4 - - + +
29D ASP* 1.3 58.8 + - - +
30D ASP 3.3 2.1 + - - -
31D HIS 4.3 5.7 + - - -
87D SER* 5.0 1.6 - - - -
161D ILE* 3.7 36.8 - - + +
164D ARG* 3.1 54.1 + - + -
165D ASN* 3.3 28.0 - - - +
168D ILE* 3.6 18.2 - - + -
174D TYR* 4.2 5.8 - + - -
213D TYR* 3.3 17.0 - + - -
214D LEU* 4.3 2.3 - - + +
217D TYR* 2.8 36.1 + + - -
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 2.9 50.3 + - + +
26D TYR* 3.9 5.4 + - - +
27D LEU 3.8 1.0 - - - -
28D TYR* 1.3 75.8 - - - +
30D ASP* 1.3 76.8 + - - +
31D HIS* 3.0 5.4 + - - +
165D ASN* 3.8 7.2 - - - +
168D ILE* 4.2 10.7 - - + +
169D ASN* 4.5 12.4 + - - +
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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