Contacts of the helix formed by residues 392 - 400 (chain A) in PDB entry 1GC5
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 GLU 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 5.3 2.0 - - - -
24A LEU* 6.4 0.2 - - - -
390A ARG* 3.0 23.8 + - + -
391A ILE* 1.3 81.8 - - + +
393A GLN* 1.3 55.5 + - + +
394A ILE 2.9 2.7 - - - -
395A ARG* 2.6 48.6 + - + +
396A ASP* 3.8 2.8 + - - +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ALA* 4.2 2.9 - - - +
385A LYS* 3.1 38.8 - - - +
387A ASN 3.5 18.6 + - - -
388A LEU* 3.6 16.7 - - + +
389A GLU* 3.8 31.8 + - - +
390A ARG* 3.1 28.0 + - + +
392A GLU* 1.3 77.2 - - + +
394A ILE* 1.3 57.1 + - - +
396A ASP* 3.0 34.3 + - - +
397A ALA 4.0 1.2 + - - -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.6 18.5 - - + -
132A VAL* 4.8 1.3 - - + -
133A TYR* 3.8 34.5 - - + +
374A PHE* 4.3 9.2 - - + -
377A LEU* 3.9 26.8 - - + +
378A ALA* 4.0 15.7 - - + +
381A ALA* 3.8 11.4 - - + -
388A LEU* 3.9 25.1 - - + -
391A ILE* 3.5 27.1 - - + +
392A GLU 2.8 0.2 + - - -
393A GLN* 1.3 75.3 - - - +
395A ARG* 1.3 63.0 + - - +
396A ASP 3.1 0.2 - - - -
397A ALA* 3.2 16.7 + - - +
398A LEU 4.2 1.2 + - - -
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.5 34.4 - - + -
21A GLU* 2.5 35.0 + - - +
24A LEU* 4.6 9.9 - - - +
392A GLU* 2.6 31.7 + - + +
394A ILE* 1.3 74.2 - - - +
396A ASP* 1.3 63.0 + - - +
398A LEU* 3.2 34.8 + - + +
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A MET* 3.9 11.5 - - + +
385A LYS* 2.8 30.4 + - - +
392A GLU 4.4 3.3 - - - +
393A GLN* 3.0 18.9 + - - +
395A ARG* 1.3 81.1 - - - +
397A ALA* 1.3 60.1 + - - +
398A LEU 3.1 1.7 + - - -
399A SER* 3.1 25.1 + - - -
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A LEU* 3.3 35.2 - - + +
380A ALA* 3.9 7.6 - - + -
381A ALA* 3.8 16.2 - - - +
384A MET* 4.1 3.3 - - - -
393A GLN 4.0 0.8 + - - -
394A ILE 3.2 12.6 + - - +
395A ARG 3.2 0.4 - - - -
396A ASP* 1.3 73.6 - - - +
398A LEU* 1.3 56.5 + - - +
399A SER 3.0 5.8 - - - -
400A VAL* 2.9 34.1 + - - +
438A LYS* 3.4 9.0 - - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS 5.1 0.4 - - - +
16A TYR* 3.9 28.9 - - + -
17A VAL* 3.9 32.8 - - + +
20A PHE* 5.1 8.1 - - + -
377A LEU* 3.9 25.9 - - + +
395A ARG* 3.2 33.3 + - + +
396A ASP 3.1 1.2 - - - -
397A ALA* 1.3 77.0 - - - +
399A SER* 1.3 59.3 + - - +
400A VAL 3.2 7.5 + - - +
438A LYS* 4.0 8.0 + - - +
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A MET* 5.5 1.2 - - - +
396A ASP 3.1 15.8 + - - -
397A ALA 3.0 0.8 - - - -
398A LEU* 1.3 77.1 - - - +
400A VAL* 1.3 68.1 + - - +
401A PRO* 3.5 9.2 - - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ALA* 4.6 1.8 - - + -
384A MET* 3.7 30.3 - - + -
397A ALA* 2.9 18.5 + - - +
398A LEU 3.9 0.5 - - - +
399A SER* 1.3 83.6 - - - +
401A PRO* 1.3 71.4 - - + +
438A LYS* 2.7 49.6 + - + +
439A ILE 3.7 23.6 - - - +
440A VAL* 4.2 15.7 - - + -
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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