Contacts of the helix formed by residues 671 - 677 (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 671 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ASN* 3.0 19.5 + - - +
609B ASP* 2.6 35.5 + - - +
610B GLU* 3.2 14.6 + - + +
670B GLY* 1.3 69.7 - - - -
672B ILE* 1.3 60.5 + - - +
673B ALA* 3.5 21.4 + - - +
674B ASP* 3.2 21.7 + - - +
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Residues in contact with ILE 672 (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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608B ASN* 3.8 12.6 - - - +
667B VAL* 4.4 8.7 - - + -
668B PRO 3.7 23.1 - - - +
669B CYS* 4.4 1.3 - - - -
670B GLY 3.1 8.0 + - - +
671B ASN* 1.3 70.8 + - - +
673B ALA* 1.3 51.2 + - - +
675B ILE* 2.8 15.3 + - + +
676B ALA* 2.7 43.4 + - + -
700B ASP* 3.6 44.2 + - + +
701B ALA* 3.7 12.6 - - + +
703B LYS* 4.7 13.5 - - + +
704B PHE* 4.1 17.3 - - + -
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Residues in contact with ALA 673 (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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671B ASN* 3.2 12.2 + - - +
672B ILE* 1.3 77.1 - - - +
674B ASP* 1.3 63.0 + - - +
675B ILE 3.3 0.5 + - - -
676B ALA* 3.7 14.3 + - - -
677B ASP* 4.3 12.7 + - - +
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Residues in contact with ASP 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ASN* 3.4 1.6 - - + -
609B ASP* 2.7 38.9 + - - +
634B TYR* 2.4 37.7 + - - -
635B SER* 5.5 0.7 + - - -
671B ASN* 3.2 23.4 + - - +
673B ALA* 1.3 79.5 - - - +
675B ILE* 1.3 58.8 + - - +
677B ASP* 5.1 0.9 + - - +
678B ASN* 4.8 5.5 + - - +
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Residues in contact with ILE 675 (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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606B LEU* 4.3 16.2 - - + +
607B LEU 3.6 29.8 - - - +
608B ASN* 4.1 12.6 - - + +
634B TYR* 4.2 13.9 - - + -
635B SER* 5.5 1.1 - - - +
654B PHE* 4.2 17.5 - - + -
667B VAL* 4.4 7.6 - - + -
672B ILE* 2.8 21.6 + - + +
674B ASP* 1.3 78.7 - - - +
676B ALA* 1.3 57.7 + - - +
677B ASP 3.2 2.9 - - - -
678B ASN* 2.8 31.7 + - + +
681B ALA* 3.9 11.2 - - + +
704B PHE* 3.8 31.3 - - + -
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Residues in contact with ALA 676 (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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672B ILE* 2.7 31.9 + - + +
673B ALA* 3.7 13.2 + - - +
675B ILE* 1.3 70.3 - - - +
677B ASP* 1.3 63.5 + - - +
682B ASN* 2.8 21.0 + - - +
703B LYS* 5.9 4.3 - - + -
704B PHE* 4.0 12.4 - - + -
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Residues in contact with ASP 677 (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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673B ALA* 4.3 11.8 + - - +
674B ASP 5.1 0.4 + - - -
675B ILE 3.2 0.4 - - - -
676B ALA* 1.3 81.7 - - - +
678B ASN* 1.3 63.5 + - - +
679B GLY* 3.2 4.6 + - - -
682B ASN* 4.1 2.2 - - - +
750C LYS* 3.8 32.1 + - + +
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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