Contacts of the helix formed by residues 16 - 25 (chain A) in PDB entry 4O14
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 ASP 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 1.3 78.5 + - - +
17A SER* 1.3 68.6 + - - +
18A TYR* 3.4 23.1 - - + -
19A LYS* 2.9 23.3 + - + +
150A THR* 2.6 30.0 + - - +
193B PHE* 4.3 9.1 - - - +
195B TYR* 3.3 23.9 + - - +
196B ARG* 3.0 29.3 + - - -
219B ASP* 3.3 16.4 - - - +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR 3.4 2.8 + - - -
16A ASP* 1.3 69.8 - - - +
18A TYR* 1.3 63.2 + - - +
20A VAL* 3.0 21.2 + - - +
87A TYR* 5.0 0.4 - - - -
90A HIS* 2.7 38.6 + - - -
91A PHE* 3.2 18.4 - - - -
219B ASP* 2.8 35.1 + - - -
221B VAL* 3.7 10.7 - - - +
241B SER* 3.7 13.0 - - - -
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.0 23.9 + - + -
17A SER* 1.3 76.4 - - - +
19A LYS* 1.3 73.6 + - + +
21A THR* 2.7 32.8 + - - -
22A HIS* 3.2 7.6 - - - -
91A PHE* 4.7 2.0 - - - -
193B PHE* 5.5 11.4 - + + -
196B ARG* 2.9 28.1 + - - -
219B ASP* 3.0 26.0 + - - +
242B VAL 4.4 9.0 - - - +
244B ALA* 3.5 42.2 - - + +
245B ALA 3.4 19.3 - - - -
246B GLU* 3.6 27.5 + - + +
311B ARG* 4.1 12.4 + - - -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.0 27.4 - - + +
16A ASP* 2.9 23.5 + - - +
18A TYR* 1.3 80.4 - - + +
20A VAL* 1.3 60.5 + - - +
21A THR 3.0 0.7 + - - -
22A HIS* 3.2 36.1 + - + +
23A TYR* 4.6 1.4 + - - -
146A ASN 2.9 25.3 + - - +
147A TRP* 3.9 19.0 - - + -
149A GLU* 2.8 28.3 + - - -
150A THR* 3.6 17.7 - - - +
196B ARG* 4.0 7.9 - - - +
246B GLU* 2.6 30.0 + - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.3 5.2 - - + -
17A SER 3.0 18.4 + - - +
19A LYS* 1.3 78.0 - - - +
21A THR* 1.3 55.0 + - + +
23A TYR* 3.2 25.1 - - - -
87A TYR* 3.4 40.2 - - + +
91A PHE* 3.9 13.7 - - + -
95A VAL* 3.7 23.0 - - - +
96A PHE* 3.9 21.1 - - + -
97A ASN 4.6 1.4 + - - -
147A TRP* 3.7 20.9 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR 2.7 19.7 + - - +
20A VAL* 1.3 79.1 - - - +
22A HIS* 1.3 61.8 + - - +
23A TYR* 3.4 3.8 - - - -
24A LYS* 3.2 16.8 + - - +
25A GLN* 2.9 26.6 + - - +
91A PHE* 4.0 15.5 - - + -
95A VAL* 3.9 32.1 - - + -
243B PRO* 3.8 20.6 - - + -
244B ALA 3.7 7.6 + - - -
269B PHE* 3.7 15.1 - - - -
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.2 23.3 + + - -
19A LYS* 3.2 35.2 + - + +
21A THR* 1.3 73.8 - - - +
23A TYR* 1.3 57.8 + - - +
24A LYS 2.9 6.3 - - - -
25A GLN* 2.8 34.8 + - - +
26A TYR* 3.3 27.5 + - + -
143A TRP* 6.1 1.3 - - + +
146A ASN* 5.7 1.4 - - - +
244B ALA 2.8 26.2 + - - -
246B GLU* 3.1 50.7 + - + +
249B THR* 3.6 12.9 - - + +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS 4.6 1.6 + - - -
20A VAL 3.2 28.0 - - - -
21A THR* 4.2 1.3 - - - -
22A HIS* 1.3 76.8 - - - +
24A LYS* 1.3 98.5 + - + +
25A GLN 3.3 0.6 + - - -
26A TYR* 4.7 3.1 + - - +
95A VAL* 3.9 11.5 - - + +
96A PHE 3.4 22.3 + - - -
97A ASN* 3.6 53.8 - - + +
142A TYR* 2.9 32.8 + - - +
143A TRP* 3.9 20.1 - - + +
147A TRP* 6.2 0.9 - + - -
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR 3.2 9.9 + - - +
22A HIS 2.9 1.6 - - - -
23A TYR* 1.3 120.1 + - + +
25A GLN* 1.3 60.8 + - - +
26A TYR 4.8 1.1 - - - -
95A VAL* 4.9 6.3 - - + +
264B HIS* 2.9 22.0 + - - -
268B GLN* 3.2 34.6 + - + +
269B PHE* 3.9 23.1 - - + -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 2.9 38.9 + - - +
22A HIS* 2.8 17.2 + - - +
24A LYS* 1.3 81.2 - - - +
26A TYR* 1.3 66.4 + - - +
244B ALA* 3.1 18.2 + - - +
245B ALA* 3.2 18.0 - - - +
249B THR* 3.1 31.0 + - - +
253B TRP* 3.0 23.0 + - - -
264B HIS* 3.7 6.3 - - - -
265B ILE* 3.8 21.6 - - + +
269B PHE* 3.8 19.7 - - + -
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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