Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 3DGG
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.8 20.4 - - + -
42A GLN 3.4 13.9 - - - +
43A LYS* 3.8 16.2 - - + +
44A PRO* 5.4 3.8 - - - -
86A ASP 3.0 11.5 + - - +
87A ALA* 1.3 77.0 - - - +
89A THR* 1.3 60.2 + - - +
90A TYR* 3.8 4.1 - - + -
106A LYS* 3.6 3.4 - - - -
107A LEU* 2.7 37.3 + - - +
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Residues in contact with THR 89 (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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40A TYR 4.1 0.2 - - - +
41A GLN* 3.6 1.9 - - - -
42A GLN* 2.8 46.1 + - - +
88A ALA* 1.3 73.5 - - - +
90A TYR* 1.3 63.3 + - - +
91A TYR* 3.6 37.0 - - + +
103A ALA 5.5 0.2 - - - +
104A GLY* 4.3 2.5 - - - -
105A THR 3.3 22.4 - - - +
106A LYS* 3.9 21.5 + - + +
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Residues in contact with TYR 90 (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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6A GLN* 2.8 26.0 + - - +
21A ILE* 3.8 27.4 - - + -
39A TRP* 5.1 1.1 - - + -
40A TYR 3.2 8.1 - - - +
41A GLN* 3.1 37.5 + - + -
51A LEU* 3.8 18.2 - - + -
66A PHE* 3.9 3.4 - + - -
77A LEU* 3.7 20.4 - - + -
79A ILE* 3.7 17.8 - - + +
86A ASP* 2.8 39.4 + - - +
88A ALA* 3.8 15.7 - - + -
89A THR* 1.3 74.2 - - - +
91A TYR* 1.3 57.2 + - - +
104A GLY* 3.2 3.5 - - - -
105A THR 2.9 23.2 + - - +
107A LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 91 (chain A).
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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6A GLN* 3.6 2.7 - - - -
39A TRP* 3.3 8.7 - - - -
40A TYR* 2.8 49.7 + - + +
42A GLN* 3.5 29.4 + - + -
48A PRO* 5.4 0.2 - - + -
89A THR* 3.6 30.2 - - + +
90A TYR* 1.3 73.7 - - - +
92A CYS* 1.3 65.9 + - - +
101A PHE* 4.3 11.9 - + + -
102A GLY 3.4 20.2 - - - -
103A ALA 3.9 7.4 + - - -
104A GLY* 3.6 18.2 - - - -
39B GLN* 3.7 5.4 + - - -
43B GLN 3.6 21.1 + - - -
44B GLY* 3.6 14.5 - - - -
45B LEU* 3.9 22.9 - - + -
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Residues in contact with CYS 92 (chain A).
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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4A LEU* 4.0 3.1 - - - -
6A GLN* 3.3 21.4 + - - -
23A CYS* 2.1 51.1 - - + -
37A MET* 3.3 15.3 - - + -
38A HIS 3.2 5.8 - - - +
39A TRP* 3.8 10.6 - - + -
91A TYR* 1.3 74.4 - - - +
93A GLN* 1.3 64.4 + - - +
101A PHE* 3.5 6.2 - - - -
102A GLY* 2.9 32.8 + - - -
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Residues in contact with GLN 93 (chain A).
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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4A LEU* 4.1 3.1 - - - -
36A TYR 3.8 0.2 - - - +
37A MET* 3.4 9.0 - - - +
38A HIS* 3.0 50.9 + - - +
40A TYR* 2.9 36.4 + - + -
92A CYS* 1.3 79.4 - - - +
94A HIS* 1.3 66.3 + - - +
95A SER* 5.9 0.7 - - - -
99A LEU* 3.8 9.6 - - + +
100A THR 3.4 13.5 - - - +
101A PHE* 3.5 25.9 - - + -
104B SER 4.6 0.5 - - - +
106B TRP* 3.3 44.5 - - - +
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Residues in contact with HIS 94 (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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2A ILE* 3.4 35.9 - - + +
4A LEU* 3.8 20.8 - - + +
29A VAL* 3.6 24.4 - - + +
36A TYR* 3.1 32.9 - - + +
37A MET* 4.6 2.2 - - - -
38A HIS* 5.3 0.9 - - - -
93A GLN* 1.3 78.8 - - - +
95A SER* 1.3 80.2 + - - +
96A ARG* 3.2 22.0 + - + +
97A GLU* 3.9 5.2 - - + -
98A LEU 4.4 1.2 + - - -
99A LEU* 3.4 3.8 - - - +
100A THR* 2.9 42.5 + - + +
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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