Contacts of the helix formed by residues 250 - 258 (chain E) in PDB entry 4GDK
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212E LEU* 4.3 26.9 - - + -
213E HIS 3.7 8.7 - - - +
214E THR* 4.3 3.4 - - + -
248E GLU 3.4 8.0 - - - +
249E THR* 1.3 85.2 - - + +
251E LEU* 1.3 66.4 + - - +
252E GLN 4.6 0.7 - - - +
253E TRP* 3.2 14.5 + - + +
254E LEU* 3.1 20.3 + - - +
13F TRP* 3.4 42.0 - - + +
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Residues in contact with LEU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ILE* 3.8 26.9 - - + -
203E PHE* 3.6 37.2 - - + -
205E PRO* 4.8 4.7 - - + -
213E HIS* 2.9 20.4 + - + +
214E THR 4.0 8.1 - - - +
215E LEU* 4.5 11.7 - - + -
218E LEU* 3.7 34.8 - - + -
249E THR 3.2 5.0 + - - -
250E PRO* 1.3 71.6 - - - +
252E GLN* 1.3 62.8 + - - +
254E LEU* 3.3 7.8 + - + +
255E SER* 3.0 23.0 + - - -
265E LEU* 4.1 18.8 - - + -
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Residues in contact with GLN 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E TYR* 4.0 2.8 - - + +
180E ASN 3.9 15.0 - - - +
181E GLY* 3.5 16.8 - - - -
182E PHE* 3.3 42.5 + - - -
185E ILE* 3.4 16.0 - - - +
205E PRO* 3.5 16.2 + - + +
212E LEU* 4.4 20.8 - - + +
213E HIS 4.5 1.0 + - - -
250E PRO 3.2 0.2 - - - -
251E LEU* 1.3 81.2 - - - +
253E TRP* 1.3 61.3 + - - +
255E SER* 3.4 3.6 + - - -
256E GLU* 2.8 57.3 + - - +
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Residues in contact with TRP 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ASP* 3.0 29.1 + - - -
7E VAL* 4.1 28.5 - - + -
249E THR* 4.4 2.2 - - + -
250E PRO* 3.2 16.0 + - + +
252E GLN* 1.3 76.2 - - - +
254E LEU* 1.3 79.8 + - + +
256E GLU* 3.1 7.4 + - - -
257E HIS* 2.9 67.0 + + + -
258E LEU* 4.3 3.8 - - + -
13F TRP* 3.5 30.5 - + + -
14F LYS* 3.4 27.6 - - + +
17F ILE* 3.5 32.8 - - + -
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Residues in contact with LEU 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.1 35.9 - - + -
240E ILE* 4.3 16.8 - - + -
245E PRO* 4.8 2.5 - - + -
249E THR* 3.6 31.2 - - + +
250E PRO 3.1 9.2 + - - +
251E LEU* 3.3 15.5 + - + +
253E TRP* 1.3 81.2 - - + +
255E SER* 1.3 57.9 + - - +
258E LEU* 2.6 67.5 + - + +
259E SER* 3.5 2.4 + - - -
265E LEU* 4.0 12.5 - - + +
17F ILE* 4.2 9.0 - - + -
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Residues in contact with SER 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LYS* 4.7 1.7 - - - +
173E MET* 4.0 8.7 - - - +
182E PHE* 3.4 23.7 - - - -
185E ILE* 3.8 28.4 - - - +
186E PRO* 4.2 7.8 + - - +
251E LEU 3.0 16.6 + - - -
252E GLN 3.6 5.6 - - - -
254E LEU* 1.3 77.1 - - - +
256E GLU* 1.3 60.7 + - - +
259E SER* 2.5 29.2 + - - -
263E ASN 5.1 1.9 + - - +
265E LEU* 4.4 5.6 - - - +
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Residues in contact with GLU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 4.0 1.0 - - - +
166E TRP* 3.8 22.5 - - - -
173E MET* 4.0 25.2 - - + +
175E TYR* 3.3 23.4 + - - -
182E PHE* 3.9 10.8 - - + -
252E GLN* 2.8 42.8 + - - +
253E TRP* 3.1 6.9 + - - +
255E SER* 1.3 78.2 - - - +
257E HIS* 1.3 87.9 + - + +
259E SER* 5.1 0.8 - - - -
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Residues in contact with HIS 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ASP* 3.3 45.1 + - + +
7E VAL* 4.5 6.9 - - + +
8E LEU* 3.5 30.1 - - + +
11E VAL* 4.1 11.8 - - - +
166E TRP* 5.6 0.6 - - - -
253E TRP* 2.9 66.4 + + + +
256E GLU* 1.3 106.1 - - + +
258E LEU* 1.3 66.0 - - - +
259E SER 3.5 4.3 - - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 3.6 32.1 - - + -
11E VAL* 3.8 16.2 - - + -
240E ILE* 4.1 17.5 - - + +
241E HIS* 2.9 27.7 + - + +
243E ILE* 4.0 26.7 - - + -
245E PRO* 5.3 1.8 - - + -
253E TRP* 4.3 7.6 - - + -
254E LEU* 2.6 45.5 + - + +
257E HIS* 1.3 75.0 - - - +
259E SER* 1.3 60.6 + - - +
260E TYR* 4.7 0.7 - - - -
265E LEU* 3.5 14.0 - - + +
17F ILE* 4.2 14.1 - - + -
21F LEU* 4.6 0.7 - - + -
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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