Contacts of the strand formed by residues 244 - 251 (chain I) in PDB entry 3GHG
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 TYR 244 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LYS* 6.0 0.3 - - - +
152I ASP* 3.1 32.8 + - + +
192I THR* 6.0 0.4 - - - -
236I ILE* 3.1 37.3 + - + -
237I SER* 3.1 23.3 - - - +
239I GLN* 3.3 15.6 + - - -
242I ILE* 3.3 29.4 - - + +
243I PRO* 1.3 75.7 - - - +
245I ALA* 1.3 61.6 - - - +
264I MET* 3.1 10.6 + - - -
265I PHE* 2.9 42.3 + - + +
266I LYS* 4.6 0.8 - - - +
386I ILE* 3.9 26.7 - - + -
387I ILE* 4.0 0.9 - - - -
388I PRO* 3.8 23.1 - - + -
389I PHE* 3.6 5.9 - - - +
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244I TYR* 1.3 77.2 - - - +
246I LEU* 1.3 64.1 + - - +
262I TYR 3.4 11.4 - - - +
265I PHE* 4.2 1.1 - - - -
386I ILE* 3.4 2.9 - - - -
387I ILE* 3.0 42.2 + - + +
389I PHE* 3.6 28.9 - - + -
392I LEU* 4.2 21.8 - - + -
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Residues in contact with LEU 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I TRP* 4.7 0.4 - - - -
194I PHE* 3.9 19.7 - - + -
245I ALA* 1.3 77.7 - - - +
247I ARG* 1.3 78.6 + - - +
248I VAL* 4.0 23.6 - - + +
261I ASP* 3.5 5.4 - - - +
262I TYR* 3.1 43.7 + - + +
265I PHE* 3.6 39.2 - - + +
278I TYR* 6.6 0.2 - - + -
290I PHE* 4.1 19.3 - - + -
384I MET* 4.3 6.7 - - + -
385I LYS 3.6 20.4 - - - +
386I ILE* 4.0 4.5 - - + -
392I LEU* 5.0 2.1 - - - +
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Residues in contact with ARG 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I TRP* 3.5 37.0 - - + +
246I LEU* 1.3 74.4 - - - +
248I VAL* 1.3 72.8 + - - +
249I GLU* 3.7 11.8 + - + -
259I THR* 3.3 19.8 + - + +
260I ALA 3.5 3.6 - - - -
261I ASP* 2.5 29.8 + - - +
383I THR 3.4 1.0 - - - +
385I LYS* 2.7 53.0 + - - +
392I LEU* 3.3 33.1 - - - +
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Residues in contact with VAL 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246I LEU* 4.0 23.3 - - + +
247I ARG* 1.3 79.6 - - - +
249I GLU* 1.3 63.4 + - - +
250I LEU* 3.1 31.0 - - + -
259I THR* 3.7 0.5 - - - -
260I ALA* 2.8 45.4 + - + +
262I TYR* 5.3 1.1 - - + -
290I PHE* 4.7 3.1 - - + -
344I LEU* 3.5 28.0 - - + -
369I TRP* 4.7 17.3 - - + -
383I THR 3.5 4.7 - - - +
384I MET* 4.1 12.1 - - + +
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Residues in contact with GLU 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I GLU* 4.7 1.7 - - - +
247I ARG* 3.7 21.6 + - + +
248I VAL* 1.3 81.5 - - - +
250I LEU* 1.3 68.3 + - - +
257I THR* 6.4 0.2 - - - -
258I SER 3.4 8.5 - - - +
259I THR* 4.3 9.2 + - + +
382I THR* 3.5 2.8 - - - -
383I THR* 2.9 58.9 + - + +
385I LYS* 2.8 36.1 + - - -
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Residues in contact with LEU 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248I VAL* 3.1 27.1 - - + -
249I GLU* 1.3 85.9 - - - +
251I GLU* 1.3 60.7 + - - +
257I THR* 3.2 25.8 - - - +
258I SER* 2.9 25.4 + - - +
286I ALA* 4.4 7.2 - - + -
344I LEU* 4.6 6.3 - - + -
369I TRP* 3.5 44.6 - - + +
372I TRP* 4.0 14.4 - - + -
379I MET* 4.0 22.9 - - + -
381I LYS* 4.3 5.2 - - - +
382I THR* 4.6 9.4 - - - +
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Residues in contact with GLU 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I LEU* 1.3 71.1 - - - +
252I ASP* 1.3 69.2 + - - +
255I GLY* 4.0 15.3 + - - -
256I ARG 3.4 12.8 - - - +
257I THR* 3.3 27.5 - - + +
372I TRP* 5.3 0.2 - - - -
379I MET* 3.0 9.4 - - - +
380I LYS* 2.7 50.8 + - - +
381I LYS* 3.1 46.6 + - + +
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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