Contacts of the strand formed by residues 308 - 314 (chain B) 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 THR 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B LEU 4.2 3.1 + - - +
303B THR* 2.9 23.8 + - - -
305B MET* 6.0 0.3 - - - +
306B GLY 2.7 22.9 + - - -
307B PRO* 1.3 71.9 + - - +
309B GLU* 1.3 60.2 + - - +
327B GLY 3.5 5.5 + - - +
328B GLY* 5.4 1.0 - - - -
329B PHE* 2.9 54.1 + - + +
330B THR* 5.9 0.4 - - - +
454B ILE* 3.8 30.1 - - + -
455B ARG 3.5 9.6 - - - +
456B PRO* 4.3 2.3 - - - +
457B PHE* 4.3 1.0 - - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TRP* 3.9 19.1 - - + -
308B THR* 1.3 74.4 - - - +
310B LEU* 1.3 59.9 + - - +
325B HIS* 3.2 22.3 + - + -
326B TYR 3.4 6.3 - - - +
327B GLY* 3.3 22.5 + - - +
454B ILE* 3.2 5.5 - - - +
455B ARG* 2.8 71.3 + - - +
456B PRO 4.2 9.3 - - - +
457B PHE* 4.5 16.2 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TRP* 4.6 0.9 - - - -
252B ILE* 4.3 1.8 - - + -
308B THR 4.0 1.4 + - - -
309B GLU* 1.3 72.2 - - - +
311B LEU* 1.3 58.0 + - - +
312B ILE* 3.6 28.0 - - + -
324B ALA 4.2 0.3 - - - +
325B HIS* 3.8 1.0 - - - -
326B TYR* 2.6 49.5 + - + +
329B PHE* 3.5 40.4 - - + -
353B LEU* 4.2 15.3 - - + -
452B MET* 3.8 25.8 - - + -
453B LYS 3.4 24.5 - - - +
454B ILE* 3.7 13.0 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B THR* 4.7 1.1 - - - +
245B GLU* 3.9 23.8 - - + +
249B TRP* 3.7 37.3 - - + -
310B LEU* 1.3 73.6 - - - +
312B ILE* 1.3 82.3 + - - +
313B GLU* 3.5 39.5 - - + +
323B LYS* 3.7 19.1 - - + -
324B ALA 3.5 11.9 - - - +
325B HIS* 4.4 11.7 - - + +
452B MET* 3.6 0.9 - - - -
453B LYS* 2.9 42.6 + - + +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU* 3.6 26.9 - - + -
311B LEU* 1.3 78.1 - - - +
313B GLU* 1.3 61.4 + - - +
314B MET* 4.0 9.0 - - + +
322B VAL 3.9 0.9 - - - +
323B LYS* 3.3 2.3 - - - -
324B ALA* 2.7 45.0 + - + +
326B TYR* 4.2 9.4 - - + -
353B LEU* 4.1 12.6 - - + -
412B PRO* 5.6 1.3 - - + -
437B TRP* 3.7 27.1 - - + -
450B MET* 3.8 23.8 - - - -
451B SER 3.2 17.3 - - - +
452B MET* 3.8 22.4 - - + -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B THR* 3.2 32.1 + - - +
245B GLU* 5.6 0.8 - - - +
311B LEU* 3.5 34.6 - - + +
312B ILE* 1.3 72.6 - - - +
314B MET* 1.3 60.7 + - - +
321B LYS* 5.8 4.9 - - + +
322B VAL 3.9 4.2 - - - -
323B LYS* 4.8 11.9 - - + +
449B LYS* 4.6 0.7 - - - +
450B MET* 3.5 2.4 + - - -
451B SER* 2.8 49.2 + - - +
453B LYS* 3.9 15.6 + - + +
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Residues in contact with MET 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ILE* 4.0 21.8 - - + +
313B GLU* 1.3 75.7 - - - +
315B GLU* 1.3 59.2 + - - +
321B LYS* 3.0 7.5 - - - +
322B VAL* 3.0 55.5 + - + +
324B ALA* 4.5 1.1 - - + -
349B ALA* 3.5 25.4 - - + -
437B TRP* 3.3 52.9 - - + -
440B TRP* 3.9 11.0 - - + -
447B MET* 3.9 10.8 - - + -
449B LYS 3.5 12.6 - - - +
450B MET* 3.9 10.1 - - - -
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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