Contacts of the helix formed by residues 251 - 256 (chain D) in PDB entry 1T9D
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 LYS 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586C TRP* 4.2 9.6 - - - -
591C TYR* 4.0 18.3 + - - -
3695C 1MM 3.0 54.0 + - - +
116D GLY 3.0 27.9 + - - +
117D ALA* 3.5 15.7 - - - +
119D LEU* 4.1 10.3 - - - +
120D PRO* 3.8 10.3 - - + -
190D GLN 2.8 14.4 + - - +
191D VAL 4.1 1.2 + - - -
192D PRO* 4.2 7.6 - - + -
249D LEU 3.4 0.4 + - - -
250D PRO* 1.3 71.7 - - - +
252D ASP* 1.3 57.4 + - - +
254D THR* 3.1 8.7 + - - -
255D ALA* 2.9 35.3 + - + +
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Residues in contact with ASP 252 (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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192D PRO* 3.2 16.0 - - + +
193D THR* 2.6 51.7 + - - +
194D SER 5.2 0.2 - - - -
250D PRO* 3.3 9.4 - - - +
251D LYS* 1.3 76.0 - - - +
253D VAL* 1.3 62.7 + - - +
255D ALA* 4.0 4.9 - - - -
256D ALA* 3.0 29.1 + - - +
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLY* 3.9 4.3 - - - -
193D THR* 4.2 4.3 - - + -
220D VAL* 3.8 26.0 - - + +
221D LYS 3.6 28.7 - - - +
222D SER* 3.7 24.9 - - - +
223D VAL* 3.7 20.2 - - - +
226D LEU* 5.3 5.4 - - + -
249D LEU* 5.8 0.7 - - + -
250D PRO* 2.9 23.4 + - + +
252D ASP* 1.3 84.9 + - - +
254D THR* 1.3 66.0 + - + +
256D ALA* 3.6 9.2 + - - -
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Residues in contact with THR 254 (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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93D THR* 3.8 3.6 - - - -
94D GLY* 3.1 14.9 + - - -
95D GLY* 2.9 25.8 + - - +
98D PHE* 6.5 0.4 - - + -
117D ALA 4.6 1.6 + - - -
118D ILE* 5.4 0.4 - - + -
120D PRO* 3.3 22.4 - - - +
121D VAL* 3.8 26.7 - - + +
226D LEU* 5.3 4.5 - - + -
249D LEU* 3.7 32.8 - - + +
250D PRO 3.2 12.2 + - - +
251D LYS* 3.1 14.0 + - - -
253D VAL* 1.3 79.3 - - + +
255D ALA* 1.3 60.5 + - - +
256D ALA 3.3 0.2 - - - -
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Residues in contact with ALA 255 (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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591C TYR* 5.7 0.4 - - - +
93D THR* 4.1 12.7 - - - +
120D PRO* 3.9 18.6 - - + -
251D LYS* 2.9 21.6 + - + +
252D ASP* 4.3 4.9 - - - +
254D THR* 1.3 77.7 + - - +
256D ALA* 1.3 65.8 + - - +
257D ILE* 3.8 3.6 + - - +
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Residues in contact with ALA 256 (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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93D THR* 3.0 3.6 - - - -
94D GLY* 2.9 26.7 + - - -
223D VAL* 4.3 14.9 - - + +
252D ASP 3.0 20.5 + - - +
253D VAL* 3.7 10.7 - - - +
254D THR 3.3 1.0 - - - -
255D ALA* 1.3 78.4 - - - +
257D ILE* 1.3 61.3 + - - +
258D LEU 4.1 0.3 + - - -
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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