Contacts of the helix formed by residues 384 - 392 (chain F) in PDB entry 6T8G
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 LEU 384 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377E LYS* 5.4 5.4 - - + -
347F LEU* 4.6 16.2 - - + -
350F PHE* 3.7 43.5 - - + -
351F GLY 5.5 0.2 - - - +
352F VAL* 5.3 7.9 - - + -
380F ARG 3.2 23.1 - - - +
381F ILE* 3.4 29.8 - - + +
382F SER 3.0 2.0 + - - -
383F ASN* 1.3 79.0 - - - +
385F ALA* 1.3 58.6 + - - +
386F LYS 3.5 2.2 - - - -
387F ASP* 3.3 21.3 + - + +
388F LEU* 2.9 34.0 + - + +
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Residues in contact with ALA 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F ILE 4.8 0.7 - - - -
382F SER 3.4 14.7 + - - +
383F ASN* 3.7 0.4 - - - +
384F LEU* 1.3 76.7 - - - +
386F LYS* 1.3 66.3 + - + +
388F LEU* 3.4 7.0 + - - +
389F ALA* 2.9 28.3 + - - +
397F VAL* 4.1 12.3 - - - +
399F VAL* 4.2 20.2 - - + -
671F GLN* 4.0 22.2 - - - +
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Residues in contact with LYS 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378E VAL* 5.6 0.4 - - - -
402E VAL* 5.9 1.7 - - + +
384F LEU 3.5 0.4 - - - -
385F ALA* 1.3 84.7 - - + +
387F ASP* 1.3 64.7 + - - +
389F ALA* 3.2 5.9 + - + +
390F ARG* 2.9 28.6 + - - +
395F ILE 4.3 4.0 + - - +
396F SER* 3.4 35.8 - - - +
397F VAL 4.9 2.5 - - - +
670F GLU 5.5 2.2 + - - -
671F GLN* 5.2 15.5 - - - +
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Residues in contact with ASP 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E LYS* 3.3 28.1 - - - +
378E VAL* 3.3 35.8 + - + +
379E SER 5.1 0.3 + - - -
350F PHE* 4.2 21.1 - - + -
383F ASN 5.0 0.2 - - - +
384F LEU* 3.6 20.2 - - + +
385F ALA 3.3 0.4 - - - -
386F LYS* 1.3 80.7 - - - +
388F LEU* 1.3 64.6 + - - +
390F ARG* 3.3 15.9 + - - +
391F SER* 3.0 23.1 + - - -
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Residues in contact with LEU 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F LEU* 5.3 2.7 - - + -
346F LYS* 4.5 11.2 - - + +
347F LEU* 3.7 37.5 - - + -
350F PHE* 4.9 4.4 - - + -
381F ILE* 5.9 1.8 - - + +
384F LEU* 2.9 25.8 + - + +
385F ALA* 3.7 6.1 - - - +
387F ASP* 1.3 76.9 - - - +
389F ALA* 1.3 61.6 + - - +
391F SER* 2.7 26.7 + - - +
392F LEU* 3.1 34.5 + - + +
397F VAL* 4.5 15.3 - - + -
399F VAL* 5.6 2.7 - - + -
411F ILE* 4.0 24.0 - - + -
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Residues in contact with ALA 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385F ALA 2.9 17.4 + - - +
386F LYS* 3.2 12.1 + - + +
388F LEU* 1.3 76.5 - - - +
390F ARG* 1.3 60.4 + - - +
392F LEU 3.4 2.3 + - - -
394F VAL* 3.2 36.6 + - + +
395F ILE 4.6 2.5 - - - +
396F SER* 4.0 13.0 - - - +
397F VAL* 3.7 33.4 - - + +
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Residues in contact with ARG 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E GLN* 5.3 1.6 - - - +
372E PRO* 3.4 28.7 - - - +
376E VAL 3.8 17.4 + - - -
378E VAL* 3.3 31.6 - - - +
401E GLU 4.5 8.7 - - - -
402E VAL* 4.8 17.2 - - + +
406E LYS 4.6 4.6 - - - +
407E THR* 3.1 52.4 + - - +
408E THR 3.8 5.8 - - - +
409E VAL* 3.7 16.2 - - - -
350F PHE* 5.1 4.4 - - - -
386F LYS 2.9 14.5 + - - +
387F ASP* 3.7 15.9 + - - +
388F LEU 3.3 0.2 - - - -
389F ALA* 1.3 78.6 - - - +
391F SER* 1.3 65.3 + - - +
392F LEU 3.3 0.5 + - - -
393F ALA* 3.5 9.2 + - - +
394F VAL 4.9 2.0 - - - -
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Residues in contact with SER 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E THR* 4.8 9.8 - - - +
342F LEU* 4.5 2.1 - - - +
346F LYS* 3.9 40.5 - - - +
350F PHE* 4.9 9.1 - - - -
387F ASP 3.0 10.4 + - - -
388F LEU* 2.7 37.2 + - - +
390F ARG* 1.3 84.8 - - - +
392F LEU* 1.3 58.2 + - - +
393F ALA 3.5 0.2 - - - -
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Residues in contact with LEU 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F MET* 4.4 22.6 - - - +
342F LEU* 3.7 28.7 - - + -
343F LEU* 4.0 18.4 - - + -
346F LYS* 4.5 7.2 - - + -
388F LEU* 3.1 40.2 + - + +
389F ALA 3.4 0.2 + - - -
390F ARG 3.2 0.6 - - - -
391F SER* 1.3 80.9 - - - +
393F ALA* 1.3 69.9 + - - +
394F VAL* 3.2 21.2 + - + +
397F VAL* 4.7 3.6 - - + -
413F ILE* 3.8 30.3 - - + -
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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