Contacts of the helix formed by residues 628 - 639 (chain C) in PDB entry 1GZL
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 TRP 628 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TRP* 3.7 21.6 - + - -
36A GLY* 3.6 26.9 - - - -
39A GLN* 3.4 40.7 - - + +
40A LEU* 4.2 21.8 - - + -
43A ARG* 5.7 8.0 - - + +
629C GLU* 1.3 63.1 + - - +
630C GLU* 3.4 5.1 - - - +
631C TRP* 3.5 62.7 - + - +
632C ASP* 3.0 27.2 + - - +
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Residues in contact with GLU 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C TRP* 1.3 75.1 - - - +
630C GLU* 1.3 56.2 + - - +
632C ASP* 3.0 0.8 + - - -
633C ARG* 2.5 69.0 + - - +
1640C N2P 1.3 64.2 + - - +
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Residues in contact with GLU 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C TRP 4.4 2.6 - - - +
629C GLU* 1.3 79.9 - - + +
631C TRP* 1.3 56.5 + - - +
633C ARG* 3.3 26.9 - - - +
634C GLU* 2.8 43.1 + - + +
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Residues in contact with TRP 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 2.7 45.8 + - + +
33A THR* 4.8 8.3 - - + -
35A TRP* 3.2 39.7 - + + -
36A GLY* 3.9 8.1 - - - +
628C TRP* 3.5 44.3 - + - +
630C GLU* 1.3 80.5 - - - +
632C ASP* 1.3 83.7 + - + +
634C GLU* 3.5 5.2 + - - +
635C ILE* 2.9 57.0 + - + +
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Residues in contact with ASP 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C TRP 3.0 19.4 + - - +
629C GLU* 3.0 3.6 + - - +
631C TRP* 1.3 93.5 - - + +
633C ARG* 1.3 65.5 + - - +
635C ILE* 3.4 12.8 + - - +
636C GLU* 3.1 6.2 - - - +
1640C N2P 2.8 62.8 + - - +
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Residues in contact with ARG 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C GLU* 2.5 50.8 + - - +
630C GLU* 3.3 38.8 - - - +
632C ASP* 1.3 72.6 - - - +
634C GLU* 1.3 62.8 + - + +
635C ILE 3.3 0.2 + - - -
636C GLU* 3.6 7.5 + - - +
637C ASN* 3.1 26.7 + - - +
1640C N2P 3.6 16.6 - - + +
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Residues in contact with GLU 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 4.6 5.2 - - - -
32A LEU* 3.3 29.9 - - + +
630C GLU* 2.8 30.0 + - + +
631C TRP 3.6 2.0 - - - +
633C ARG* 1.3 79.7 - - + +
635C ILE* 1.3 62.9 + - - +
637C ASN* 3.3 18.8 - - - +
638C TYR* 3.0 50.3 + - + +
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Residues in contact with ILE 635 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.7 11.5 - - + +
32A LEU* 3.7 30.3 - - + -
33A THR* 5.1 4.9 - - + +
631C TRP* 2.9 53.7 + - + +
632C ASP* 3.5 16.6 - - - +
633C ARG 3.2 0.6 - - - -
634C GLU* 1.3 79.8 - - - +
636C GLU* 1.3 63.4 + - + +
639C THR* 2.7 36.2 + - - +
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Residues in contact with GLU 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632C ASP* 3.1 7.4 - - - +
633C ARG* 3.6 8.1 - - - +
635C ILE* 1.3 78.3 - - + +
637C ASN* 1.3 59.1 + - - +
639C THR* 3.4 21.1 - - - +
1640C N2P 1.3 60.1 + - - +
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Residues in contact with ASN 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 5.7 1.0 - - - -
633C ARG 3.1 18.8 + - - +
634C GLU* 3.3 25.0 - - - +
635C ILE 3.1 0.2 - - - -
636C GLU* 1.3 80.3 - - - +
638C TYR* 1.3 77.8 + - - +
639C THR 3.8 4.3 - - - +
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Residues in contact with TYR 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 5.6 1.2 - - - +
25A ARG* 3.8 52.9 - - + +
28A LYS* 3.6 47.3 - - + +
29A LEU* 3.5 24.4 - - + +
32A LEU* 4.2 4.5 - - + -
634C GLU* 3.0 44.6 + - - -
637C ASN* 1.3 89.5 - - - +
639C THR* 1.3 61.5 + - - +
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Residues in contact with THR 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 6.0 0.4 - - - -
29A LEU* 3.2 25.8 - - + +
635C ILE* 2.7 28.5 + - - +
636C GLU* 3.4 17.8 + - - +
637C ASN 3.3 4.8 - - - +
638C TYR* 1.3 80.0 - - - +
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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