Contacts of the helix formed by residues 377 - 383 (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 LYS 377 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 4.6 9.2 - - + -
383A ASN* 5.2 11.0 + - - +
384A LEU* 3.8 26.5 - - + +
387A ASP* 3.3 11.4 - - + +
390A ARG* 5.2 0.4 - - - -
376F VAL* 1.3 89.0 - - - +
378F VAL* 1.3 67.4 + - - +
379F SER* 3.3 12.8 - - - +
380F ARG* 3.3 38.4 + - + +
381F ILE* 3.5 5.8 + - - +
1G A 5.5 8.3 + - - -
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Residues in contact with VAL 378 (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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386A LYS* 5.7 6.3 - - + -
387A ASP* 3.5 16.3 + - + +
390A ARG* 3.4 39.9 - - + +
377F LYS* 1.3 75.7 - - - +
379F SER* 1.3 57.8 + - - +
381F ILE* 2.9 12.2 + - + +
382F SER* 2.8 31.5 + - - +
399F VAL* 5.7 1.6 - - + -
400F VAL 4.8 0.2 - - - +
401F GLU* 3.5 39.7 - - + +
409F VAL* 4.2 14.1 - - + -
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Residues in contact with SER 379 (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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377F LYS* 4.1 13.9 - - - +
378F VAL* 1.3 77.1 - - - +
380F ARG* 1.3 63.5 + - - +
382F SER* 3.4 12.5 - - - -
383F ASN* 2.9 37.0 + - - +
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Residues in contact with ARG 380 (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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351F GLY* 2.4 41.0 + - - -
352F VAL* 4.1 15.8 - - + +
375F GLY 3.4 23.4 + - - -
376F VAL* 4.2 4.6 - - - +
377F LYS* 3.3 37.6 + - + +
378F VAL 3.2 0.6 - - - -
379F SER* 1.3 81.5 + - - +
381F ILE* 1.3 62.7 + - - +
382F SER 3.4 0.2 + - - -
383F ASN* 3.7 7.2 + - - +
384F LEU* 3.2 20.1 + - - +
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Residues in contact with ILE 381 (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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347F LEU* 5.1 9.2 - - + -
352F VAL* 3.8 36.6 - - + -
354F VAL* 5.9 3.6 - - + -
372F PRO* 5.8 5.4 - - + -
376F VAL* 4.4 8.3 - - + -
377F LYS 3.8 12.1 - - - +
378F VAL* 2.9 13.1 + - + +
380F ARG* 1.3 74.6 - - - +
382F SER* 1.3 63.5 + - - +
384F LEU* 3.4 19.6 + - + +
385F ALA 4.5 0.9 + - - -
388F LEU* 5.9 1.9 - - + +
399F VAL* 3.7 30.3 - - + +
409F VAL* 5.0 17.7 - - + -
411F ILE* 4.5 20.6 - - + -
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Residues in contact with SER 382 (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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378F VAL* 2.8 21.0 + - - +
379F SER* 3.2 15.7 + - - -
381F ILE* 1.3 79.8 - - - +
383F ASN* 1.3 68.0 + - - +
384F LEU 3.0 6.3 + - - -
385F ALA* 3.4 19.4 + - - +
399F VAL* 4.2 15.5 + - - +
401F GLU* 4.5 13.5 + - - +
671F GLN* 5.0 3.5 + - - -
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Residues in contact with ASN 383 (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* 5.1 7.4 - - - +
379F SER* 2.9 24.4 + - - +
380F ARG* 4.0 5.0 - - - +
382F SER* 1.3 83.2 + - - +
384F LEU* 1.3 59.7 + - - +
385F ALA 3.7 0.9 - - - +
387F ASP* 5.0 1.0 - - - +
657F LYS* 5.6 5.5 - - - +
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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