Contacts of the helix formed by residues 381 - 386 (chain B) in PDB entry 1GGE
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 ASN 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B PRO* 4.4 2.2 - - - -
380B ASP* 1.3 79.1 + - - +
382B PHE* 1.3 67.7 + - - +
383B PHE* 3.3 11.7 + - - +
384B ALA* 2.8 32.9 + - + +
385B GLU* 2.9 29.2 + - - +
225C PRO* 3.8 25.8 + - - +
226C HIS 4.2 0.2 - - - -
445D ARG* 4.1 19.1 - - - +
446D ASP* 4.2 6.1 + - - +
450D ARG* 5.9 0.5 - - - +
452D GLY 5.8 0.2 - - - -
453D ILE* 4.1 13.5 - - + -
454D ASP* 3.8 20.8 + - - +
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Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLY 3.4 11.4 - - - -
132B SER* 4.8 2.0 - - - -
133B ALA 5.3 0.2 - - - -
165B ARG* 5.9 0.4 - - - -
319B ARG* 3.5 34.8 - - + -
323B TRP* 5.6 2.7 - + - -
379B PRO* 4.9 6.7 - - + -
381B ASN* 1.3 71.4 - - - +
383B PHE* 1.3 64.6 + - + +
386B ASN* 2.7 71.1 + - + +
387B GLU* 3.0 25.4 + - + -
225C PRO* 3.0 15.0 + - + +
226C HIS 3.3 17.2 + - - +
227C TRP* 3.5 17.7 - - - -
228C ALA* 3.4 19.7 - - + -
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU 3.9 7.2 - - - -
121B ARG* 5.3 0.7 - - - -
122B ILE* 3.9 31.6 - - + -
381B ASN* 3.3 5.0 + - - +
382B PHE* 1.3 84.5 - - - +
384B ALA* 1.3 67.9 + - + +
387B GLU* 3.3 23.0 - - + +
388B GLN* 3.2 45.9 + - + +
225C PRO 4.6 1.0 + - - -
446D ASP* 3.2 49.6 - - + +
447D GLY 3.4 31.9 - - - -
450D ARG* 3.9 5.6 - - + -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ASN* 2.8 27.7 + - + +
383B PHE* 1.3 76.8 - - - +
385B GLU* 1.3 58.7 + - - +
388B GLN* 3.1 35.2 + - - +
431B ILE* 4.4 1.7 - - - +
432B PRO* 6.1 0.3 - - - +
433B ILE* 3.9 9.0 + - - +
450D ARG* 4.7 9.2 - - + +
452D GLY 4.3 10.5 - - - +
453D ILE* 4.0 25.4 - - + +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 4.3 5.3 - - + +
72B ARG* 5.3 0.7 + - - -
135B HIS* 2.8 30.7 + - - -
163B PHE* 3.3 25.2 - - + -
377B ARG* 4.5 2.8 + - - -
379B PRO* 3.6 18.3 - - + +
380B ASP* 2.7 32.5 + - - +
381B ASN 2.9 18.1 + - - +
384B ALA* 1.3 81.4 - - - +
386B ASN* 1.3 65.9 + - - +
389B ALA* 3.3 12.5 + - - +
433B ILE* 3.4 18.2 - - + +
453D ILE* 3.5 27.9 - - + +
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Residues in contact with ASN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG* 2.9 17.5 + - - -
131B GLY 3.1 14.3 + - - -
132B SER* 3.5 0.8 - - - +
133B ALA* 3.3 32.9 - - + +
163B PHE* 4.2 7.8 - - + -
165B ARG* 3.0 21.9 + - - +
379B PRO* 5.2 4.5 - - + -
382B PHE* 2.7 58.8 + - + +
385B GLU* 1.3 74.7 - - - +
387B GLU* 1.3 69.3 + - - +
389B ALA* 3.1 8.5 + - - +
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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