Contacts of the helix formed by residues 393 - 398 (chain H) 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 GLN 393 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H THR 5.1 1.0 - - - +
378H TYR* 3.8 12.5 - - - +
379H ASP* 5.5 0.9 - - - -
380H ARG 5.6 0.2 + - - -
381H ASP* 3.4 36.3 + - + +
383H ASP* 3.5 6.3 - - - +
385H TRP* 3.3 8.8 - - - -
389H ASP 5.0 0.6 + - - +
390H PRO* 3.2 27.9 + - + +
391H ARG 2.9 6.5 + - - +
392H LYS* 1.3 77.0 - - - +
394H CYS* 1.3 66.4 + - - +
395H SER* 4.7 1.8 - - - +
396H LYS* 3.2 46.4 + - + +
397H GLU* 3.8 5.2 + - - +
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Residues in contact with CYS 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383H ASP* 2.9 26.4 + - + +
385H TRP* 3.5 4.8 - - - -
393H GLN* 1.3 71.2 - - - +
395H SER* 1.3 58.5 + - - +
396H LYS 3.3 0.5 + - - -
397H GLU* 3.4 2.3 + - - +
398H ASP* 3.1 32.6 + - - +
404H TYR* 3.6 26.2 - - + -
406H ARG* 3.3 23.1 - - - -
407H CYS* 2.1 48.9 - - - -
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Residues in contact with SER 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376H SER* 3.5 13.0 + - - -
377H THR* 3.3 40.6 - - - -
378H TYR* 3.3 12.3 + - - +
393H GLN* 3.4 2.1 - - - +
394H CYS* 1.3 75.5 - - - +
396H LYS* 1.3 64.8 + - - +
398H ASP 4.3 1.3 - - - -
399H GLY* 3.9 7.8 + - - -
400H GLY 2.4 38.3 + - - +
404H TYR* 3.9 9.2 - - - -
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Residues in contact with LYS 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378H TYR* 4.0 30.5 - - + +
390H PRO* 3.1 37.9 + - - +
391H ARG* 3.7 19.0 - - + +
393H GLN* 3.2 38.3 + - + +
394H CYS 3.2 1.0 - - - -
395H SER* 1.3 80.5 - - - +
397H GLU* 1.3 63.0 + - + +
399H GLY* 4.2 5.0 + - - -
429H HIS* 4.0 16.8 + - + +
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Residues in contact with GLU 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H TRP* 3.2 20.5 - - + -
391H ARG* 3.5 19.1 - - - +
392H LYS* 5.7 0.2 - - - +
393H GLN 3.9 4.3 - - - +
394H CYS 3.9 6.5 - - - +
396H LYS* 1.3 79.7 - - + +
398H ASP* 1.3 63.3 + - - +
399H GLY* 3.3 4.5 + - - -
429H HIS* 3.5 38.5 + - + +
431H THR* 3.1 30.8 + - + +
433H ASP* 3.1 15.4 - - - +
3S ARG* 2.7 29.7 + - - +
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Residues in contact with ASP 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H CYS 3.1 16.7 + - - +
397H GLU* 1.3 74.5 - - - +
399H GLY* 1.3 58.3 + - - +
400H GLY 3.6 1.8 - - - -
404H TYR* 3.2 21.1 + - + +
407H CYS* 3.8 4.0 - - - +
408H HIS* 2.9 28.1 + - - -
411H ASN* 2.6 34.4 + - - +
414H GLY* 3.8 1.7 - - - -
431H THR* 2.7 21.7 + - - +
432H ASP* 4.3 0.2 - - - -
433H ASP* 3.4 13.4 - - - +
3S ARG* 2.4 33.6 + - - -
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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