Contacts of the helix formed by residues 384 - 388 (chain X) in PDB entry 1G3I
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 VAL 384 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380X ALA 3.1 23.1 - - - +
381X ALA* 3.9 8.3 - - - +
382X PHE 2.8 1.0 - - - -
383X ARG* 1.3 83.9 - - + +
385X ASN* 1.3 62.8 + - - +
386X GLU 3.2 1.8 - - - -
387X LYS* 3.4 5.6 + - - -
388X THR* 2.9 33.6 + - - +
395X ARG* 3.2 39.5 - - - +
399X VAL* 5.6 2.5 - - + -
430X LEU* 6.6 0.2 - - + -
433X VAL* 5.3 18.8 - - + -
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Residues in contact with ASN 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R GLN* 3.0 12.8 + - - -
341X PHE* 4.2 7.1 - - - -
381X ALA 3.5 11.8 - - - +
382X PHE* 2.8 15.8 + - + +
384X VAL* 1.3 75.8 - - - +
386X GLU* 1.3 56.9 + - - +
387X LYS 3.2 2.9 - - - -
388X THR 2.9 17.5 - - - +
389X GLU 3.3 12.9 + - - -
390X ASN* 2.7 42.4 + - - +
391X ILE 4.0 1.0 - - - +
392X GLY* 3.6 17.2 + - - +
395X ARG* 2.8 37.2 - - - +
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Residues in contact with GLU 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R GLN* 4.2 5.6 - - - +
70R HIS* 3.1 22.1 + - - +
382X PHE* 3.2 33.4 + - + +
383X ARG* 4.9 12.0 + - - +
384X VAL 3.2 0.6 - - - +
385X ASN* 1.3 77.5 - - - +
387X LYS* 1.3 69.5 + - + +
388X THR 3.7 0.9 - - - -
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Residues in contact with LYS 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R HIS* 4.1 7.4 - - - -
383X ARG* 3.4 48.2 - - + +
384X VAL* 3.4 4.5 + - - +
385X ASN 3.2 0.6 - - - -
386X GLU* 1.3 92.3 - - + +
388X THR* 1.3 71.3 + - - +
433X VAL* 4.2 21.5 - - + -
434X VAL* 4.5 2.4 - - - +
435X GLU* 3.2 55.8 + - + +
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Residues in contact with THR 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R GLN* 3.4 9.6 + - - +
70R HIS* 4.1 7.2 - - - -
317W SER* 5.1 7.9 - - - -
384X VAL* 2.9 22.1 + - - +
385X ASN 2.9 13.6 - - - +
386X GLU 3.7 0.6 - - - -
387X LYS* 1.3 83.0 + - - +
389X GLU* 1.3 86.8 + - - +
390X ASN 3.3 0.9 + - - -
395X ARG* 4.7 6.3 - - - -
433X VAL* 6.1 0.5 - - - +
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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