Contacts of the strand formed by residues 49 - 54 (chain A) in PDB entry 1GNZ
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 ALA 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.5 5.9 - - - -
25A ASP* 2.9 23.9 + - - +
35A LEU 4.1 2.9 - - - -
36A CYS* 4.4 1.3 - - - -
48A SER* 1.3 76.4 - - - +
50A GLY* 1.3 58.4 + - - +
101A VAL* 3.6 24.7 - - + -
102A LYS 4.1 10.1 - - - +
104A ALA* 4.2 15.0 - - + -
109A GLY* 4.2 6.7 - - - -
218A ALA 3.4 9.6 - - - +
219A SER* 4.1 0.2 - - - +
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN 3.4 10.3 - - - -
24A GLY* 4.4 0.2 - - - -
26A ALA 3.8 1.8 - - - -
35A LEU* 3.1 28.0 + - - +
49A ALA* 1.3 76.0 - - - +
51A ARG* 1.3 66.0 + - - +
101A VAL* 4.5 0.8 - - - +
217A SER* 3.1 3.3 - - - -
218A ALA 2.9 33.6 + - - -
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE 3.6 1.0 - - - +
23A GLN* 2.7 63.1 + - + +
26A ALA* 3.3 9.1 - - - +
35A LEU* 3.8 0.7 - - - -
50A GLY* 1.3 81.0 - - - +
52A ALA* 1.3 62.3 + - - +
53A LEU* 4.1 4.8 - - + +
93A PHE* 3.8 22.4 - - + -
99A SER* 3.3 26.1 + - - -
100A ASP 3.2 27.9 + - - -
101A VAL* 3.6 15.0 - - + +
102A LYS* 4.5 1.8 - - - +
109A GLY* 2.9 29.2 + - - -
110A LEU* 3.9 18.2 + - - +
216A ILE 3.2 9.4 - - - +
217A SER* 3.2 17.3 - - - -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.0 16.2 - - + -
21A ILE 3.4 4.7 - - - -
22A PHE* 4.3 7.0 - - + -
26A ALA* 4.7 0.4 - - - -
33A LEU* 3.7 34.3 - - + -
35A LEU* 3.8 4.6 - - + +
51A ARG* 1.3 73.9 - - - +
53A LEU* 1.3 61.0 + - - +
215A GLY* 3.1 4.5 - - - -
216A ILE 2.8 31.8 + - - +
233A TRP* 4.1 8.0 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.5 6.0 - - - -
21A ILE* 2.7 51.6 + - + +
23A GLN* 3.3 40.4 - - + +
51A ARG* 4.3 2.5 - - + +
52A ALA* 1.3 76.9 - - - +
54A TYR* 1.3 68.0 + - - +
93A PHE* 3.2 38.8 - - + -
95A ALA* 6.1 0.9 - - + -
96A PRO 5.8 0.2 - - - +
97A PRO 5.1 4.3 - - - +
99A SER* 3.9 10.1 - - - +
213A ARG* 4.3 23.3 - - + +
214A VAL 3.5 5.8 - - - +
215A GLY* 3.8 10.8 - - - +
233A TRP* 4.9 0.4 - - - -
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.8 13.5 - - + -
6A SER 4.4 4.5 + - - -
7A PHE* 3.3 65.2 - + + +
9A PHE* 4.1 11.2 - + - -
19A SER* 3.4 35.3 - - - -
20A ILE* 4.3 3.1 - - + -
53A LEU* 1.3 70.2 - - - +
55A SER* 1.3 61.6 + - - +
56A ASP* 3.2 58.0 + - + +
213A ARG* 3.4 22.3 - - - +
214A VAL* 2.9 22.8 + - + +
233A TRP* 4.3 3.7 - - + -
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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