Contacts of the helix formed by residues 641 - 649 (chain B) in PDB entry 1GPU
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 LYS 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS 6.0 0.2 + - - -
26A ALA 4.3 16.4 + - - -
27A ASN* 5.6 2.8 - - - +
94A ARG 4.1 0.8 + - - -
95A GLN* 3.4 27.1 + - - +
96A LEU 4.8 1.6 - - - +
476B GLU* 3.7 20.6 + - - +
640B GLY* 1.3 70.5 - - - -
642B ALA* 1.3 65.8 + - - +
643B PRO* 4.1 9.6 - - + -
644B GLU* 2.9 44.4 + - + +
645B VAL* 3.0 9.9 + - - +
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Residues in contact with ALA 642 (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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472B ILE 4.5 1.1 - - - -
473B GLY* 3.5 31.9 - - - +
475B GLY* 3.9 13.1 - - - -
476B GLU* 4.4 2.2 + - - +
528B ARG* 4.7 3.6 - - - +
529B GLN* 6.1 3.8 - - + -
640B GLY 3.2 3.4 + - - -
641B LYS* 1.3 69.4 - - - +
643B PRO* 1.3 71.0 - - + +
645B VAL* 3.0 6.9 + - - +
646B PHE* 3.0 34.0 + - + -
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Residues in contact with PRO 643 (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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641B LYS* 3.4 11.2 - - + -
642B ALA* 1.3 95.4 - - + +
644B GLU* 1.3 60.7 + - + +
646B PHE* 3.5 9.8 + - + +
647B LYS* 3.1 41.3 + - - +
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Residues in contact with GLU 644 (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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95A GLN* 4.7 4.9 - - - +
96A LEU* 3.8 36.1 + - + +
641B LYS* 2.9 42.5 + - + +
643B PRO* 1.3 76.4 - - + +
645B VAL* 1.3 61.0 + - - +
647B LYS* 3.4 12.0 + - + +
648B PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 645 (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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96A LEU* 4.6 9.2 - - + -
472B ILE* 3.7 33.7 - - + +
475B GLY* 4.7 3.4 - - - -
638B ALA* 3.9 24.5 - - + +
640B GLY* 3.5 24.5 - - - +
641B LYS 3.0 14.3 + - - +
642B ALA* 3.0 8.5 + - - +
644B GLU* 1.3 74.3 - - - +
646B PHE* 1.3 65.3 + - - +
648B PHE* 3.1 14.5 + - - +
649B PHE* 3.1 36.0 + - + -
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Residues in contact with PHE 646 (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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471B SER* 4.2 2.2 - - - -
472B ILE* 3.6 18.8 - - + -
473B GLY* 3.5 31.2 - - - -
529B GLN* 3.4 30.3 - - + -
564B SER* 4.9 1.1 - - - -
565B GLU* 4.2 9.6 - - - -
568B LEU* 6.2 0.4 - - + -
617B VAL* 3.8 28.0 - - + -
642B ALA* 3.0 32.0 + - + -
643B PRO* 3.7 9.6 - - + +
645B VAL* 1.3 76.9 - - - +
647B LYS* 1.3 61.1 + - + +
649B PHE* 3.2 4.5 + - - +
650B GLY 3.2 4.0 + - - -
651B PHE* 2.9 44.1 + - + +
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Residues in contact with LYS 647 (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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643B PRO* 3.1 31.1 + - - +
644B GLU* 3.7 10.8 - - + +
646B PHE* 1.3 73.8 - - + +
648B PHE* 1.3 67.3 + - - +
650B GLY* 2.9 14.5 + - - +
652B THR* 4.1 29.8 - - + +
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Residues in contact with PHE 648 (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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96A LEU* 4.0 31.0 - - + -
635B ARG* 3.9 30.7 - - - -
638B ALA* 5.1 4.5 - - + -
644B GLU 2.9 13.6 + - - +
645B VAL* 3.1 10.1 + - - +
647B LYS* 1.3 77.5 - - - +
649B PHE* 1.3 90.6 + + - +
650B GLY 3.5 0.5 + - - -
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Residues in contact with PHE 649 (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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472B ILE* 3.8 22.9 - - + -
631B PHE* 3.7 8.7 - - - -
633B ILE* 3.6 26.2 - - + -
635B ARG* 3.3 36.1 - - + -
636B PHE 3.6 19.7 - - - -
637B GLY* 4.1 8.3 - - - -
638B ALA* 4.8 0.7 - - + -
645B VAL* 3.1 37.9 + - + +
646B PHE 3.2 3.3 + - - +
647B LYS 3.1 0.6 - - - -
648B PHE* 1.3 93.3 - + - +
650B GLY* 1.3 59.5 + - - +
651B PHE* 3.3 33.1 - - + -
659B ARG* 4.7 2.6 + - - -
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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