Contacts of the helix formed by residues 431 - 435 (chain A) 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 ILE 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ALA 4.4 1.1 - - - +
388A GLN* 3.6 40.6 - - + +
423A LEU* 3.9 34.3 - - + +
428A PHE* 3.2 26.4 + - - +
430A GLU* 1.3 75.0 - - - +
432A PRO* 1.3 76.8 - - + +
433A ILE* 4.3 8.1 - - + +
434A ASN* 2.8 24.0 + - - +
435A ARG 3.3 7.1 + - - -
449C HIS* 3.4 37.2 - - + +
450C ARG 4.4 0.9 - - - +
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Residues in contact with PRO 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 2.8 23.4 + - - -
68A LEU* 3.6 21.4 - - + +
71A VAL* 3.7 18.2 - - + -
384A ALA 6.1 0.2 - - - +
430A GLU 3.2 6.9 - - - +
431A ILE* 1.3 88.3 - - + -
433A ILE* 1.3 58.5 + - - +
434A ASN 3.2 0.9 + - - -
435A ARG* 3.2 22.5 + - - +
450C ARG 4.3 1.6 - - - +
451C MET* 3.5 49.6 - - + +
453C ILE* 4.2 6.5 - - + -
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 3.3 10.5 + - - +
68A LEU* 4.1 7.3 - - + +
135A HIS* 3.6 31.4 - - + +
163A PHE* 3.9 23.6 - - + -
188A LYS* 4.2 1.0 - - + +
190A TYR* 2.7 36.8 + - - +
384A ALA 3.8 13.6 + - - +
385A GLU* 3.4 40.6 - - + +
388A GLN 4.2 1.1 - - - -
389A ALA* 3.8 13.0 - - + +
431A ILE* 3.3 4.0 - - + +
432A PRO* 1.3 77.0 - - - +
434A ASN* 1.3 75.8 + - - +
453C ILE* 5.3 1.2 - - - +
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Residues in contact with ASN 434 (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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188A LYS* 3.9 13.4 + - - +
190A TYR* 4.8 1.3 - - - -
195A ILE* 4.1 10.0 - - - +
388A GLN 3.0 24.3 + - - -
389A ALA* 3.5 5.7 - - - -
390A ALA* 2.9 40.9 + - - +
423A LEU* 4.0 3.2 - - - +
428A PHE* 3.2 27.1 + - + +
429A HIS* 3.8 9.0 - - - +
431A ILE* 2.8 23.2 + - - +
433A ILE* 1.3 74.1 - - - +
435A ARG* 1.3 62.5 + - - +
436A PRO* 3.4 5.7 - - - +
84C GLN* 4.4 9.2 - - - +
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Residues in contact with ARG 435 (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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64A LYS* 2.8 25.0 + - - +
67A SER* 3.1 21.8 + - - -
68A LEU* 4.0 11.5 - - - +
70A ASP* 2.7 41.8 + - - -
71A VAL* 4.2 8.1 - - - +
190A TYR* 3.5 8.5 - - - -
195A ILE* 4.4 0.7 - - - -
429A HIS 3.4 14.6 - - - +
430A GLU* 3.7 15.7 - - - +
431A ILE 3.3 6.9 + - - +
432A PRO* 3.2 26.2 + - - +
434A ASN* 1.3 76.8 - - - +
436A PRO* 1.3 78.0 - - + +
451C MET* 4.5 7.3 - - - +
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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