Contacts of the helix formed by residues 427 - 431 (chain D) 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 427 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 2.8 24.6 + - - -
449B HIS* 3.2 16.2 - - + -
425D GLY 3.3 2.0 - - - -
426D PRO* 1.3 76.9 - - - +
428D PHE* 1.3 57.3 + - - +
429D HIS* 3.1 9.2 - - - -
430D GLU* 2.8 39.3 + - - +
446D ASP 2.9 22.6 + - - -
447D GLY* 3.3 9.9 + - - -
448D MET 3.1 25.7 + - - +
449D HIS 4.1 3.1 - - - +
450D ARG* 3.0 23.7 + - - +
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Residues in contact with PHE 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLN* 3.8 24.0 - - - -
112B GLU* 6.3 3.1 - - + -
115B THR* 6.1 0.9 - - + -
449B HIS* 4.4 1.1 - - - -
390D ALA* 4.2 21.1 - - + -
395D HIS* 4.7 10.8 - + - -
415D TYR 5.3 0.2 - - - -
416D THR* 4.4 27.8 - - + -
419D GLN* 4.0 27.8 - - + -
420D ILE* 5.1 2.9 - - + -
423D LEU* 3.7 31.1 + - + -
425D GLY 3.4 18.2 + - - +
426D PRO* 3.2 14.0 - - + -
427D ASN* 1.3 76.7 - - - +
429D HIS* 1.3 65.5 + - + +
430D GLU 3.1 0.2 - - - -
431D ILE* 3.3 18.5 + - - +
434D ASN* 3.1 23.4 + - - -
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Residues in contact with HIS 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASN* 3.5 51.3 + - + +
84B GLN* 4.0 18.8 - - - +
116B HIS* 4.5 1.3 - + - -
426D PRO 3.5 18.8 + - - -
427D ASN* 3.7 19.7 - - - -
428D PHE* 1.3 83.9 - - + +
430D GLU* 1.3 64.1 + - + +
431D ILE 3.3 1.3 - - - -
434D ASN* 4.1 10.8 - - - +
435D ARG* 3.3 28.2 - - - +
436D PRO* 4.2 1.9 - - + +
440D TYR* 2.9 42.6 + + - -
450D ARG* 4.3 2.9 - - - -
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Residues in contact with GLU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B HIS* 4.0 8.1 - - - +
451B MET* 3.6 12.8 - - - +
427D ASN* 2.8 37.4 + - - +
429D HIS* 1.3 93.3 - - + +
431D ILE* 1.3 65.1 + - - +
432D PRO* 3.2 7.1 - - - +
435D ARG* 3.7 13.4 - - - +
440D TYR* 4.2 7.0 + - + +
449D HIS 3.4 3.1 - - - +
450D ARG* 3.5 12.8 + - - -
451D MET* 2.7 33.5 + - + +
452D GLY* 2.8 26.5 + - - -
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Residues in contact with ILE 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B MET* 6.4 0.2 - - - -
449B HIS* 3.4 37.2 - - + +
450B ARG 4.1 1.1 - - - +
384D ALA 4.4 1.3 - - - +
388D GLN* 3.4 42.0 - - + +
423D LEU* 4.1 33.2 - - + +
428D PHE* 3.3 23.8 + - - +
430D GLU* 1.3 78.6 - - - +
432D PRO* 1.3 77.5 - - + +
433D ILE* 4.3 10.8 - - + -
434D ASN* 2.9 20.1 + - - +
435D ARG 3.3 5.7 + - - -
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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
------------------------------------------------------------
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