Contacts of the helix formed by residues 250 - 258 (chain A) in PDB entry 4TQ1
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 4.4 26.0 - - + -
213A HIS 3.6 8.5 - - - +
214A THR* 4.2 3.8 - - + -
248A GLU 3.5 7.6 - - - +
249A THR* 1.3 88.1 - - + +
251A LEU* 1.3 65.5 + - - +
252A GLN 3.3 1.1 - - - +
253A TRP* 3.4 15.4 + - + +
254A LEU* 3.2 20.8 + - - +
578B TRP* 3.3 41.5 - - + +
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Residues in contact with LEU 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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185A ILE* 3.8 27.8 - - + -
203A PHE* 3.5 37.2 - - + -
205A PRO* 5.0 3.4 - - + -
213A HIS* 2.8 25.4 + - + +
214A THR 4.3 4.0 - - - +
215A LEU* 4.8 5.8 - - + -
218A LEU* 4.1 28.5 - - + -
249A THR 3.4 3.4 + - - -
250A PRO* 1.3 69.8 - - - +
252A GLN* 1.3 60.1 + - - +
254A LEU* 3.1 14.7 + - + +
255A SER* 2.9 27.9 + - - -
265A LEU* 3.8 23.3 - - + -
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Residues in contact with GLN 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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175A TYR* 3.6 13.9 - - + +
180A ASN 4.0 11.9 - - - +
181A GLY* 3.2 10.3 - - - -
182A PHE* 2.9 53.5 + - - +
185A ILE* 3.7 0.8 - - - +
205A PRO* 3.5 23.3 + - + +
212A LEU* 4.5 20.1 - - + +
213A HIS 4.6 1.0 + - - -
250A PRO* 3.3 1.2 - - - +
251A LEU* 1.3 77.2 - - - +
253A TRP* 1.3 63.1 + - - +
255A SER* 3.2 6.2 + - - -
256A GLU* 2.8 50.3 + - - +
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Residues in contact with TRP 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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4A ASP* 2.9 36.6 + - - -
7A VAL* 4.1 13.5 - - + -
212A LEU* 6.2 0.2 - - - +
249A THR* 4.3 2.5 - - + -
250A PRO* 3.4 21.2 + - + +
251A LEU 3.2 0.4 - - - -
252A GLN* 1.3 79.0 - - - +
254A LEU* 1.3 77.5 + - + +
256A GLU* 3.2 9.3 + - - -
257A HIS* 2.9 63.4 + + + -
258A LEU* 4.1 17.0 - - + -
578B TRP* 3.6 36.8 - + + -
579B ARG* 3.4 14.8 - - - +
582B ILE* 4.0 31.4 - - + -
583B PHE* 5.2 1.8 - + - -
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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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215A LEU* 4.0 35.0 - - + -
240A ILE* 4.5 9.2 - - + -
245A PRO* 4.3 9.9 - - + -
249A THR* 3.6 31.9 - - + +
250A PRO 3.2 10.1 + - - +
251A LEU* 3.1 17.6 + - + +
253A TRP* 1.3 86.6 - - + +
255A SER* 1.3 58.4 + - - +
258A LEU* 2.7 63.0 + - + +
259A SER 3.4 2.4 + - - -
265A LEU* 3.6 14.8 - - + +
582B ILE* 4.9 0.4 - - + -
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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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136A LYS* 4.5 1.9 + - - +
173A MET* 3.6 7.1 - - - +
182A PHE* 3.4 21.2 - - - -
185A ILE* 3.8 28.0 - - - +
186A PRO* 3.9 13.9 + - - +
251A LEU 2.9 13.4 + - - -
252A GLN 3.6 7.9 - - - -
254A LEU* 1.3 76.2 - - - +
256A GLU* 1.3 61.6 + - - +
259A SER* 2.6 32.0 + - - -
263A ASN 5.0 0.5 + - - -
265A LEU* 3.8 6.0 - - - +
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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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8A LEU* 3.8 2.4 - - - +
166A TRP* 3.8 23.6 - - - -
173A MET* 3.8 24.4 - - + +
175A TYR* 3.4 18.0 + - - -
182A PHE* 3.9 11.0 - - + -
252A GLN* 2.8 50.2 + - - +
253A TRP* 3.2 6.1 + - - -
255A SER* 1.3 78.2 - - - +
257A HIS* 1.3 89.0 + - + +
259A SER 5.1 0.2 + - - -
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Residues in contact with HIS 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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4A ASP* 3.6 42.7 + - + +
7A VAL* 4.1 6.8 - - + +
8A LEU* 3.7 27.6 - - + +
11A VAL* 3.9 14.2 - - - +
166A TRP* 6.1 0.2 - - - -
253A TRP* 2.9 67.7 + + + +
256A GLU* 1.3 106.8 - - + +
258A LEU* 1.3 67.0 + - - +
259A SER 3.5 2.9 - - - +
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Residues in contact with LEU 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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7A VAL* 3.6 22.2 - - + -
11A VAL* 4.0 9.2 - - + -
240A ILE* 4.1 20.7 - - + +
241A HIS* 2.8 34.1 + - + -
243A ILE* 4.1 24.7 - - + -
245A PRO* 4.3 6.7 - - + -
253A TRP* 4.1 15.3 - - + -
254A LEU* 2.7 42.0 + - + +
257A HIS* 1.3 79.6 - - - +
259A SER* 1.3 62.4 + - - +
260A TYR* 3.8 1.4 + - - -
265A LEU* 3.6 13.2 - - + +
582B ILE* 4.6 7.0 - - + -
586B LEU* 5.4 0.9 - - + -
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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