Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 1D1T
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A THR 3.5 4.2 - - - +
248A LYS* 1.3 88.0 - - + +
250A ILE* 1.3 66.7 + - - +
251A SER* 3.8 16.6 - - - +
252A GLU* 3.1 39.8 + - + +
253A VAL* 3.1 9.2 + - - +
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Residues in contact with ILE 250 (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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198A PHE* 4.3 8.3 - - + -
222A ILE* 4.2 13.0 - - + -
241A ILE* 4.0 27.4 - - + -
242A SER 5.0 0.9 - - - +
243A PRO* 4.3 31.4 - - + +
248A LYS 3.5 1.4 + - - -
249A PRO* 1.3 71.8 - - - +
251A SER* 1.3 61.4 + - - +
253A VAL* 3.1 13.1 + - + +
254A LEU* 2.8 41.2 + - + +
277A ASP* 3.9 34.7 + - + +
281A SER* 3.9 10.3 - - - +
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Residues in contact with SER 251 (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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249A PRO* 3.8 13.3 - - - +
250A ILE* 1.3 82.2 - - - +
252A GLU* 1.3 58.8 + - - +
254A LEU* 3.5 1.7 + - - +
255A SER* 3.0 28.2 + - - -
277A ASP* 4.9 1.6 - - - -
280A ALA* 3.4 36.5 - - - +
281A SER* 3.3 20.2 - - - +
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Residues in contact with GLU 252 (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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248A LYS* 3.8 23.1 + - + +
249A PRO* 3.1 38.3 + - + +
251A SER* 1.3 80.6 + - - +
253A VAL* 1.3 62.1 + - - +
255A SER* 3.1 6.6 + - - -
256A GLU* 2.8 46.0 + - - +
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Residues in contact with VAL 253 (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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241A ILE* 4.4 12.1 - - + -
246A SER* 4.3 13.5 - - - +
248A LYS* 3.4 31.0 - - + +
249A PRO 3.3 15.7 - - - +
250A ILE* 3.1 14.7 + - + +
252A GLU* 1.3 77.2 - - - +
254A LEU* 1.3 58.0 + - - +
256A GLU* 3.3 10.5 + - - +
257A MET* 2.9 49.0 + - + +
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Residues in contact with LEU 254 (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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196A VAL* 3.8 30.5 - - + -
198A PHE* 3.8 12.1 - - + -
220A ILE* 4.2 12.8 - - + -
222A ILE* 3.9 9.9 - - + -
241A ILE* 4.1 13.5 - - + -
250A ILE* 2.8 34.5 + - + +
251A SER* 3.9 3.4 - - - +
253A VAL* 1.3 73.1 - - - +
255A SER* 1.3 63.8 + - - +
257A MET* 3.3 10.5 + - - +
258A THR* 3.0 27.8 + - - +
262A VAL* 4.2 13.5 - - + -
281A SER* 3.3 32.5 - - - +
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Residues in contact with SER 255 (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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251A SER 3.0 18.5 + - - -
252A GLU* 3.5 8.1 - - - -
254A LEU* 1.3 76.2 - - - +
256A GLU* 1.3 55.5 + - - +
258A THR* 3.2 4.9 + - - -
259A GLY* 2.7 31.9 + - - -
260A ASN* 2.8 38.1 + - - +
262A VAL* 4.8 3.3 - - - +
281A SER 5.6 0.8 + - - -
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Residues in contact with GLU 256 (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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248A LYS* 3.1 41.6 + - - +
252A GLU* 2.8 31.9 + - + +
253A VAL* 3.7 6.4 - - - +
255A SER* 1.3 76.0 - - - +
257A MET* 1.3 63.8 + - - +
258A THR 3.3 0.2 + - - -
259A GLY* 3.4 8.7 + - - -
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Residues in contact with MET 257 (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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218A ARG* 2.6 30.1 + - - +
220A ILE* 3.8 18.2 - - + -
239A GLU* 3.6 38.6 - - + +
241A ILE* 3.8 34.5 - - + -
253A VAL* 2.9 26.0 + - + +
254A LEU* 3.4 17.3 - - - +
255A SER 3.2 0.2 - - - -
256A GLU* 1.3 78.7 - - - +
258A THR* 1.3 54.0 + - + +
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Residues in contact with THR 258 (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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194A THR* 3.7 28.9 - - + -
218A ARG* 3.6 22.6 + - - +
220A ILE* 4.0 9.2 - - + -
254A LEU 3.0 17.5 + - - +
255A SER* 3.4 3.1 + - - -
257A MET* 1.3 77.7 - - - +
259A GLY* 1.3 62.0 + - - +
260A ASN 3.7 0.2 + - - -
261A ASN* 3.2 37.8 + - - +
262A VAL* 3.6 13.3 - - + +
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Residues in contact with GLY 259 (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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255A SER 2.7 9.3 + - - -
256A GLU* 3.4 10.1 + - - -
257A MET 3.6 0.2 - - - -
258A THR* 1.3 73.1 - - - +
260A ASN* 1.3 68.7 + - - +
261A ASN* 4.1 0.3 - - - +
101B ASN* 3.0 17.3 + - - -
995B CAC 3.1 10.7 - - - +
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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