Contacts of the helix formed by residues 381 - 386 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ARG* 4.3 18.9 - - - +
446A ASP* 4.2 6.5 + - - +
450A ARG* 5.8 0.5 - - - +
452A GLY 5.8 0.4 - - - -
453A ILE* 4.1 7.2 - - + -
454A ASP* 3.8 21.1 + - - +
225B PRO* 3.7 25.7 + - - +
226B HIS 4.0 0.7 - - - -
379C PRO* 4.5 1.6 - - - -
380C ASP* 1.3 79.3 + - - +
382C PHE* 1.3 66.8 + - - +
383C PHE* 3.3 11.0 + - - +
384C ALA* 2.7 39.9 + - + +
385C GLU* 3.0 28.3 + - - +
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Residues in contact with PHE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B PRO 3.0 17.2 + - - +
226B HIS 3.2 15.2 + - - +
227B TRP* 3.5 18.6 - - - -
228B ALA* 3.4 20.6 - - + +
131C GLY 3.4 1.8 - - - -
132C SER* 4.8 2.0 - - - -
165C ARG* 5.8 0.4 - - - -
319C ARG* 3.4 44.9 - - + -
323C TRP* 5.6 3.1 - + - -
379C PRO* 5.0 6.1 - - + -
381C ASN* 1.3 70.2 - - - +
383C PHE* 1.3 63.2 + - + +
386C ASN* 2.7 70.1 + - + +
387C GLU* 3.0 25.6 + - + -
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Residues in contact with PHE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ASP* 3.2 45.3 - - - +
447A GLY 3.4 30.7 - - - -
450A ARG* 3.9 4.7 - - + -
225B PRO 4.6 0.6 + - - -
120C GLU 3.9 11.2 - - - -
121C ARG* 5.3 1.3 - - - -
122C ILE* 3.8 41.1 - - + -
381C ASN* 3.3 5.8 + - - +
382C PHE* 1.3 82.0 - - + +
384C ALA* 1.3 71.2 + - + +
387C GLU* 3.8 20.6 - - + -
388C GLN* 3.1 43.9 + - + +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ARG* 4.7 8.7 - - + +
452A GLY 4.4 10.1 - - - +
453A ILE* 4.1 23.4 - - + +
381C ASN* 2.7 31.3 + - + +
382C PHE 3.4 0.2 - - - -
383C PHE* 1.3 75.4 - - - +
385C GLU* 1.3 59.4 + - - +
388C GLN* 3.2 36.7 + - - +
431C ILE* 4.5 1.0 - - - +
433C ILE* 3.9 8.7 + - - +
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Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A ILE* 3.6 27.9 - - + +
68C LEU* 4.2 5.5 - - - +
72C ARG* 5.2 1.1 + - - -
135C HIS* 2.7 30.3 + - - -
163C PHE* 3.2 26.6 - - + -
377C ARG* 4.6 2.8 + - - -
379C PRO* 3.6 13.5 - - + +
380C ASP* 2.6 35.5 + - - +
381C ASN 3.0 19.5 + - - +
384C ALA* 1.3 79.8 - - + +
386C ASN* 1.3 62.7 + - - +
389C ALA* 3.3 13.4 - - - +
433C ILE* 3.4 20.1 - - + +
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Residues in contact with ASN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 2.9 17.7 + - - -
131C GLY 3.2 21.5 + - - +
132C SER* 3.5 0.8 - - - +
133C ALA* 3.2 33.0 - - + +
163C PHE* 4.2 7.4 - - + -
165C ARG* 3.0 22.3 + - - +
379C PRO* 5.3 4.7 - - + -
382C PHE* 2.7 50.2 + - + +
385C GLU* 1.3 73.6 - - - +
387C GLU* 1.3 69.5 + - - +
389C ALA* 3.0 9.2 + - - +
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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