Contacts of the helix formed by residues 55 - 63 (chain D) in PDB entry 2GRA
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 HIS 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D SER* 4.3 0.2 - - - -
53D THR* 2.9 19.6 - - + +
54D PRO* 1.3 102.7 + - + +
56D ASN* 1.3 65.5 + - - +
57D LYS* 3.2 5.1 + - + +
58D GLU* 3.1 44.1 + - + +
59D THR* 3.4 6.9 + - - -
81D GLU* 5.6 0.2 - - - -
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Residues in contact with ASN 56 (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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6D ILE* 3.4 24.5 - - + +
7D GLY* 4.3 0.5 + - - -
33D SER* 2.6 38.5 + - - -
35D PRO* 5.2 9.1 - - - +
54D PRO 4.8 5.8 + - - -
55D HIS* 1.3 68.0 - - - +
57D LYS* 1.3 61.7 + - - +
59D THR* 3.2 10.4 - - - -
60D VAL* 3.0 21.0 - - - +
78D ILE* 4.2 9.0 - - + +
81D GLU* 3.2 34.8 + - - +
82D ILE* 3.5 11.2 - - + -
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Residues in contact with LYS 57 (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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55D HIS* 3.2 3.7 - - + -
56D ASN* 1.3 73.2 - - - +
58D GLU* 1.3 68.5 + - - +
59D THR 2.9 1.3 - - - -
60D VAL* 2.9 19.3 + - - +
61D GLN* 3.1 20.6 + - + +
81D GLU* 3.3 24.9 + - - +
82D ILE* 3.5 10.1 - - + -
84D ALA* 5.5 3.6 - - - +
85D ASP* 3.0 41.4 + - + +
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Residues in contact with GLU 58 (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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31D MET* 3.0 19.6 - - + +
53D THR* 2.9 38.4 + - + +
55D HIS* 3.1 31.8 + - + +
57D LYS* 1.3 78.4 - - - +
59D THR* 1.3 67.3 + - - +
61D GLN* 3.4 19.9 + - - +
62D HIS* 3.2 9.4 + - - +
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Residues in contact with THR 59 (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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4D GLY* 4.1 20.6 - - - -
5D PHE 4.2 3.4 - - - +
6D ILE* 3.7 8.7 - - + -
31D MET* 3.4 23.9 - - + +
32D ALA 4.2 0.3 - - - -
33D SER* 2.7 27.5 + - - +
53D THR* 5.0 1.0 + - - -
55D HIS 3.4 5.4 + - - -
56D ASN 3.2 10.8 - - - -
57D LYS 2.9 0.4 + - - -
58D GLU* 1.3 76.5 - - - +
60D VAL* 1.3 55.9 + - - +
62D HIS* 2.4 36.6 + - - +
63D SER 3.1 3.6 + - - -
66D LEU* 3.7 25.1 - - + -
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Residues in contact with VAL 60 (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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6D ILE* 4.6 1.1 - - + -
56D ASN 3.0 19.1 - - - +
57D LYS* 2.9 9.4 + - - +
59D THR* 1.3 73.0 - - - +
61D GLN* 1.3 61.4 + - + +
63D SER* 3.1 13.0 + - - -
66D LEU* 4.3 15.7 - - + -
82D ILE* 3.1 37.0 - - + -
85D ASP* 3.7 21.8 - - + +
86D ILE* 4.4 1.8 - - + -
90D HIS* 2.7 52.1 - - + +
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Residues in contact with GLN 61 (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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57D LYS* 3.5 16.9 - - + +
58D GLU* 3.6 23.8 - - - +
59D THR 2.8 1.8 + - - -
60D VAL* 1.3 75.7 - - + +
62D HIS* 1.3 56.9 + - - +
63D SER 3.2 0.2 + - - -
85D ASP* 6.0 4.0 - - + +
87D GLU* 6.4 0.9 - - - -
89D ARG* 2.8 23.8 + - - +
90D HIS* 5.0 1.3 - - - -
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Residues in contact with HIS 62 (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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2D SER* 3.4 19.2 - - - -
3D VAL 3.6 4.8 + - - -
28D HIS 3.9 15.0 + - - -
29D LYS* 3.4 27.6 - - - +
30D ILE 3.5 21.0 + - - -
31D MET* 3.2 39.5 - - + +
51D LYS* 4.4 11.9 + - + +
58D GLU 3.2 1.1 + - - +
59D THR 2.4 20.0 + - - +
61D GLN* 1.3 73.2 - - - +
63D SER* 1.3 55.3 + - - -
64D ASP* 4.3 0.9 - - - -
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Residues in contact with SER 63 (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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2D SER 3.9 2.5 - - - -
4D GLY* 3.5 22.0 - - - -
59D THR 3.1 2.4 + - - -
60D VAL* 3.1 15.3 + - - -
61D GLN 3.1 1.2 - - - -
62D HIS* 1.3 80.5 - - - +
64D ASP* 1.3 52.0 - - - +
65D VAL 3.3 19.7 - - - -
66D LEU* 3.2 21.5 - - - +
89D ARG* 3.2 5.4 + - - -
90D HIS* 2.6 41.1 + - - -
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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