Contacts of the helix formed by residues 240 - 250 (chain T) in PDB entry 5GJQ
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 SER 240 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433S ASP* 5.6 1.4 - - - +
436S PHE* 4.4 12.0 - - - -
236T LEU* 5.6 1.1 - - - +
238T GLU 5.1 0.4 - - - -
239T GLY* 1.3 75.8 - - - -
241T TYR* 1.3 59.6 + - - +
242T ASN 3.1 2.9 - - - +
243T LYS* 2.6 32.8 + - - +
244T VAL* 2.8 14.1 + - - +
267T ILE* 4.1 26.9 - - - +
271T ILE* 4.4 15.7 - - - -
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Residues in contact with TYR 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430S SER* 6.2 1.1 - - - -
432S GLU* 5.2 13.9 - - + -
433S ASP* 4.8 17.6 - - - +
240T SER* 1.3 76.7 - - - +
242T ASN* 1.3 63.3 + - - +
244T VAL* 3.4 9.4 + - - +
245T PHE* 3.1 21.0 + - - +
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Residues in contact with ASN 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433S ASP* 5.6 5.7 - - - -
235T TYR* 4.0 25.8 - - + -
239T GLY* 6.0 0.9 - - - -
240T SER 3.1 2.3 - - - +
241T TYR* 1.3 76.7 - - - +
243T LYS* 1.3 63.8 + - - +
245T PHE* 3.1 21.9 - - - +
246T LEU* 3.2 6.2 + - - +
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Residues in contact with LYS 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232T LEU* 4.7 21.4 - - + +
235T TYR* 4.4 12.5 - - + +
236T LEU* 4.9 9.4 - - + -
240T SER* 2.6 26.2 + - - +
242T ASN* 1.3 70.8 - - - +
244T VAL* 1.3 54.4 + - - +
246T LEU* 2.6 38.3 + - - +
247T ALA* 3.1 4.4 + - - +
267T ILE* 4.2 18.4 - - + -
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Residues in contact with VAL 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240T SER 2.8 12.8 + - - +
241T TYR* 3.6 12.6 - - - +
243T LYS* 1.3 71.2 - - - +
245T PHE* 1.3 58.7 + - - +
247T ALA* 2.8 33.2 + - - +
248T LYS* 3.2 6.6 + - - +
267T ILE* 4.9 8.0 - - + +
292T PHE* 5.3 13.5 - - + -
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Residues in contact with PHE 245 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241T TYR 3.1 13.3 + - - +
242T ASN* 3.1 17.0 - - - +
243T LYS 3.0 0.6 + - - -
244T VAL* 1.3 75.1 - - - +
246T LEU* 1.3 60.6 + - - +
248T LYS* 3.1 18.3 + - - +
249T GLY* 3.2 10.0 + - - -
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Residues in contact with LEU 246 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228T HIS* 5.1 12.8 - - + +
231T SER* 6.4 1.1 - - - -
232T LEU* 4.2 30.3 - - + +
242T ASN 3.2 5.3 + - - +
243T LYS* 2.6 23.9 + - - +
245T PHE* 1.3 70.5 - - - +
247T ALA* 1.3 57.8 + - - -
249T GLY* 2.9 18.4 + - - +
250T ASN* 3.2 13.2 + - - +
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Residues in contact with ALA 247 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232T LEU* 5.3 4.6 - - + +
243T LYS 3.1 5.3 + - - +
244T VAL* 2.8 20.3 + - - +
246T LEU* 1.3 77.7 - - - +
248T LYS* 1.3 59.0 + - - +
249T GLY 3.4 0.2 + - - -
250T ASN* 3.6 14.9 + - - +
251T ILE 4.7 1.4 + - - -
260T ILE* 4.7 23.5 - - + +
264T LEU* 6.2 4.7 - - + -
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Residues in contact with LYS 248 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244T VAL 3.2 5.6 + - - +
245T PHE* 3.1 12.7 + - - +
247T ALA* 1.3 78.6 - - - +
249T GLY* 1.3 58.9 + - - +
250T ASN 3.4 0.7 + - - -
251T ILE* 3.9 17.9 - - - +
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Residues in contact with GLY 249 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228T HIS* 6.1 1.3 - - - -
245T PHE 3.2 8.3 + - - -
246T LEU* 2.9 11.5 + - - -
248T LYS* 1.3 76.5 - - - +
250T ASN* 1.3 60.8 + - - +
251T ILE* 3.2 2.6 + - - -
252T PRO* 3.9 15.7 - - - +
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Residues in contact with ASN 250 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228T HIS* 5.2 14.1 - - + -
246T LEU 3.2 7.9 + - - +
247T ALA* 3.9 12.6 - - - +
248T LYS 3.4 1.2 - - - -
249T GLY* 1.3 75.6 - - - +
251T ILE* 1.3 50.6 + - - +
252T PRO* 3.0 6.5 - - - -
253T ALA* 2.1 54.5 + - + +
256T TYR* 4.8 8.5 - - + -
257T THR* 6.0 2.5 - - - +
260T ILE* 4.7 15.5 - - + -
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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