Contacts of the helix formed by residues 170 - 180 (chain D) in PDB entry 4KYI
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 ASN 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D MET* 4.2 20.5 - - - +
162D GLU* 2.4 41.6 + - - +
163D THR* 3.9 8.7 - - + -
168D ALA 3.4 2.8 + - - -
169D MET* 1.3 83.7 - - - +
171D VAL* 1.3 54.2 + - - +
173D GLU* 3.3 29.1 + - - +
174D ILE* 2.6 36.2 + - - +
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Residues in contact with VAL 171 (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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37D LEU* 3.8 39.7 - - + +
40D ARG* 3.7 24.7 - - + -
41D PHE* 4.1 13.5 - - + +
163D THR* 4.4 2.5 - - - -
164D SER 3.9 10.1 - - - +
165D ALA* 4.2 0.2 - - - -
168D ALA* 3.6 24.1 + - + +
169D MET 2.8 16.9 + - - +
170D ASN* 1.3 76.1 - - - +
172D ASN* 1.3 62.6 + - - +
173D GLU* 3.6 0.4 + - - -
174D ILE* 3.2 11.4 - - - +
175D PHE* 3.1 28.7 - - + -
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Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 4.1 24.3 - - + -
63D VAL* 5.1 3.3 - - - +
168D ALA 4.6 1.7 + - - +
171D VAL* 1.3 80.8 - - - +
173D GLU* 1.3 74.1 + - - +
175D PHE* 3.6 2.6 + - - +
176D MET* 3.2 35.3 + - - +
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Residues in contact with GLU 173 (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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161D MET* 4.0 12.9 - - + +
168D ALA 4.2 4.1 - - - +
170D ASN* 3.3 41.0 + - - +
171D VAL 3.2 0.6 + - - -
172D ASN* 1.3 89.9 + - - +
174D ILE* 1.3 57.3 + - - +
176D MET* 3.6 6.7 + - - +
177D ALA* 3.1 26.9 + - - +
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Residues in contact with ILE 174 (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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37D LEU* 6.4 0.7 - - + -
98D ILE* 4.7 10.5 - - + -
130D ALA* 4.6 21.3 - - + -
131D LEU 4.7 1.8 - - - +
132D ALA* 3.8 31.2 - - + -
159D LEU* 5.1 4.7 - - + +
161D MET* 3.7 31.6 - - + +
163D THR* 4.2 9.4 - - + -
170D ASN 2.6 18.0 + - - +
171D VAL* 3.2 21.1 - - - +
173D GLU* 1.3 72.4 - - - +
175D PHE* 1.3 76.0 + - + +
177D ALA* 3.3 5.1 + - + +
178D ILE* 3.2 29.6 + - + +
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Residues in contact with PHE 175 (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 LEU* 3.6 35.7 - - + -
26D LEU* 4.9 11.0 - - + -
37D LEU* 5.0 6.7 - - + -
38D VAL* 5.3 5.6 - - + -
41D PHE* 3.8 53.4 - + + -
72D PHE* 3.8 22.5 - + + -
74D ILE* 4.2 10.1 - - + -
98D ILE* 3.6 21.3 - - + -
171D VAL* 3.1 29.2 - - + -
172D ASN 3.6 3.3 + - - +
173D GLU 3.4 0.2 - - - -
174D ILE* 1.3 83.7 - - + +
176D MET* 1.3 62.6 + - + +
177D ALA 3.1 0.2 - - - -
178D ILE* 3.2 8.3 + - + +
179D ALA* 3.0 25.6 + - - +
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Residues in contact with MET 176 (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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67B ASP* 5.4 8.5 - - + +
63D VAL* 4.1 31.0 - - + -
64D CYS 4.2 12.6 - - - +
65D LEU* 3.8 28.9 - - + -
70D VAL* 6.4 0.2 - - + -
172D ASN* 3.2 32.9 + - - +
173D GLU* 3.9 6.7 - - - +
174D ILE 3.3 0.4 - - - -
175D PHE* 1.3 77.8 - - + +
177D ALA* 1.3 60.4 + - - +
179D ALA* 3.7 7.9 - - + +
180D LYS* 3.3 45.6 + - - +
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Residues in contact with ALA 177 (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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159D LEU* 3.3 24.4 - - + +
161D MET* 4.1 16.2 - - + -
173D GLU 3.1 17.0 + - - +
174D ILE* 3.4 13.0 - - + +
175D PHE 3.1 0.2 - - - -
176D MET* 1.3 78.4 - - - +
178D ILE* 1.3 58.2 + - - +
180D LYS* 4.0 8.4 + - - +
181D LYS* 3.3 25.3 + - - +
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Residues in contact with ILE 178 (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 LEU* 4.6 11.0 - - + -
72D PHE* 5.0 4.9 - - + -
96D ALA* 3.6 27.6 - - + -
97D ALA 4.2 4.3 - - - +
98D ILE* 3.8 34.3 - - + -
128D VAL* 3.9 16.8 - - + +
130D ALA* 4.1 20.4 - - + -
159D LEU* 4.8 4.9 - - + -
174D ILE* 3.2 17.0 - - + +
175D PHE* 3.2 8.6 + - - +
177D ALA* 1.3 77.0 - - - +
179D ALA* 1.3 64.7 + - - +
180D LYS 3.3 0.4 - - - -
181D LYS* 3.3 15.1 + - - +
182D LEU* 3.4 19.4 - - + +
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Residues in contact with ALA 179 (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 PHE* 6.5 0.7 - - - -
65D LEU* 3.5 23.9 - - + +
70D VAL* 4.4 18.9 - - + +
72D PHE* 4.3 15.0 - - + -
175D PHE 3.0 16.4 + - - +
176D MET* 3.7 18.8 - - + +
177D ALA 3.4 0.2 - - - -
178D ILE* 1.3 78.9 - - - +
180D LYS* 1.3 60.2 + - - +
182D LEU* 3.2 24.0 + - - +
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Residues in contact with LYS 180 (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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67B ASP* 6.2 1.8 - - - +
65D LEU* 3.6 20.1 - - + +
176D MET* 3.3 39.3 + - - +
177D ALA* 4.3 8.3 - - - +
178D ILE 3.3 0.4 - - - -
179D ALA* 1.3 73.8 - - - +
181D LYS* 1.3 60.1 + - + +
182D LEU* 3.0 12.1 + - - -
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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