Contacts of the helix formed by residues 624 - 628 (chain B) in PDB entry 1GXD
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 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B ILE 5.3 5.8 - - - +
445B VAL* 6.5 0.2 - - - -
446B PHE* 4.6 20.2 - - + -
449B ILE* 5.2 1.1 - - + -
458B PHE* 5.8 0.7 - - + -
603B PHE* 3.5 31.4 - - + -
604B LYS 5.7 0.9 - - - +
605B GLY 4.9 4.3 - - - +
606B ALA* 4.1 23.5 + - + +
607B TYR* 3.7 6.1 - - - +
608B TYR* 3.4 29.8 - - + +
623B SER* 1.3 68.6 + - - +
625B LYS* 1.3 63.5 + - + +
626B SER 2.9 7.2 + - - -
628B TRP* 3.2 21.0 + - + +
629B LEU* 2.8 39.3 + - + +
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Residues in contact with LYS 625 (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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439B ILE 3.8 16.8 - - - +
440B CYS 3.4 17.8 + - - -
441B LYS 5.2 0.8 - - - -
443B ASP* 2.7 46.6 + - + +
444B ILE 4.7 3.6 - - - +
606B ALA* 5.0 6.7 + - + +
623B SER* 3.1 11.0 - - - +
624B ILE* 1.3 86.3 - - + +
626B SER* 1.3 59.1 + - - +
629B LEU* 3.6 19.1 - - + -
631B CYS* 2.9 35.7 - - - -
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Residues in contact with SER 626 (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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623B SER* 3.1 24.3 + - - -
624B ILE 2.9 0.2 - - - -
625B LYS* 1.3 84.2 + - - +
627B ASP* 1.3 61.9 + - - +
629B LEU 3.6 8.5 - - - +
630B GLY 4.1 8.0 - - - +
631B CYS 3.8 20.3 + - - +
137D PRO* 6.4 1.3 - - - -
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Residues in contact with ASP 627 (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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470B PRO* 3.3 29.5 - - - +
601B TYR* 4.9 5.2 - - - -
608B TYR* 3.2 37.7 + - + +
620B LYS* 4.8 7.9 + - - -
623B SER 2.9 13.3 + - - +
626B SER* 1.3 77.7 - - - +
628B TRP* 1.3 70.0 + - + +
629B LEU 4.4 0.2 - - - -
630B GLY 5.8 0.2 - - - -
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Residues in contact with TRP 628 (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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449B ILE* 5.3 1.6 - - + -
451B GLN* 5.7 1.8 - - - -
456B ILE* 4.6 28.7 - - + -
458B PHE* 3.6 29.8 - + + -
467B THR* 5.0 5.0 - - - +
470B PRO* 4.6 20.5 - - + +
474B PRO* 4.3 11.1 - - - +
592B VAL* 4.4 8.3 - - + -
593B ASP* 3.9 13.5 - - - -
601B TYR* 3.3 42.8 - + + -
603B PHE* 3.2 34.2 - + - -
608B TYR* 3.3 29.2 - + - -
624B ILE* 3.2 27.1 + - + +
627B ASP* 1.3 89.9 + - - +
629B LEU* 1.3 66.9 + - - +
630B GLY 3.8 1.8 + - - -
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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