Contacts of the strand formed by residues 34 - 41 (chain D) in PDB entry 3Q3G
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 ILE 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D PHE* 3.9 29.8 - - + -
30D ASN 3.9 8.7 - - - +
31D ILE* 3.1 29.6 - - + +
32D LYS 3.5 2.7 + - - +
33D ASP* 1.3 82.8 - - + +
35D TYR* 1.3 61.2 + - - +
36D MET* 3.6 49.1 - - + +
54D ASP* 4.6 1.0 - - - +
55D PRO* 3.2 14.2 - - + +
100D SER* 4.1 11.7 - - - +
101D GLU 3.7 7.2 - - - +
102D GLY* 4.0 17.0 - - - -
103D HIS* 3.9 10.2 - - - -
104D TYR* 5.7 1.6 - - - +
113D TYR* 6.1 1.1 - - + -
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Residues in contact with TYR 35 (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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100C TYR* 4.5 0.9 - - - -
34D ILE* 1.3 70.0 - - - +
36D MET* 1.3 61.6 + - - +
37D GLN* 3.6 16.9 + - - +
52D ARG* 3.9 19.8 + - - -
53D ILE 3.4 3.8 - - - -
54D ASP* 3.6 41.9 + - + -
100D SER* 3.4 3.8 - - - -
101D GLU* 2.9 58.9 + - + +
103D HIS* 3.5 29.4 - + - -
177G SER* 4.8 0.2 + - - -
178G GLU* 3.4 37.1 + - - +
179G GLU* 4.9 2.6 - - - +
205G LEU 4.0 3.9 + - - -
206G LEU 3.2 24.1 + - - -
207G GLY* 3.7 5.5 - - - -
208G ARG* 4.2 0.4 - - - -
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Residues in contact with MET 36 (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 LEU* 4.1 15.9 - - + -
24D CYS* 4.0 17.5 - - - +
26D PRO* 3.8 16.6 - - + -
31D ILE* 3.6 31.0 - - + -
34D ILE* 3.6 17.3 + - + +
35D TYR* 1.3 71.2 - - - +
37D GLN* 1.3 67.9 + - - +
38D TRP* 4.5 6.3 - - - +
52D ARG* 3.1 3.4 - - - -
53D ILE* 2.9 54.3 + - + +
55D PRO* 4.8 2.0 - - + -
81D ALA* 3.6 25.4 - - + -
98D CYS* 4.6 5.8 - - + -
99D ALA 3.6 12.3 - - - +
100D SER* 4.2 2.7 - - - -
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Residues in contact with GLN 37 (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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100C TYR* 5.1 0.6 + - - -
102C LEU* 3.3 15.5 - - - +
35D TYR* 3.6 20.0 - - - +
36D MET* 1.3 74.3 - - - +
38D TRP* 1.4 65.2 + - - +
39D VAL* 4.3 1.1 - - + -
49D TRP* 2.7 34.3 + - + +
51D GLY 3.5 4.3 - - - -
52D ARG* 3.4 16.8 - - - +
98D CYS* 3.2 8.7 - - - +
99D ALA* 2.6 42.1 + - + +
101D GLU* 3.5 32.6 + - - +
111D MET* 4.0 31.0 - - + -
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Residues in contact with TRP 38 (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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8D GLN* 3.8 20.4 - - - -
22D LEU* 4.1 21.5 - - + -
23D SER 4.1 7.2 - - - -
24D CYS* 3.8 29.8 - - + -
36D MET* 4.5 5.1 - - - +
37D GLN* 1.4 76.5 + - - +
39D VAL* 1.4 58.2 + - - +
49D TRP* 3.8 1.4 - - - -
50D ILE* 2.8 44.4 + - + +
51D GLY 3.0 12.6 + - - +
72D ILE* 3.6 38.0 - - + +
81D ALA* 3.8 18.8 - - - +
82D TYR 3.5 14.3 + - - +
83D LEU* 3.5 38.4 - - + -
96D TYR* 4.5 8.3 - - + -
97D TYR 3.4 19.3 - - - -
98D CYS* 3.9 8.1 - - + -
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Residues in contact with VAL 39 (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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104C PHE* 4.3 11.2 - - + -
37D GLN* 4.8 1.1 - - + -
38D TRP* 1.4 78.0 - - - +
40D LYS* 1.3 61.6 + - - +
47D LEU* 3.8 28.7 - - + -
48D GLU 3.5 25.4 - - - +
49D TRP* 4.4 8.7 - - + -
50D ILE* 4.3 3.8 - - - +
95D VAL 3.9 0.5 - - - +
96D TYR* 3.5 2.3 - - - -
97D TYR* 2.8 42.6 + - + +
99D ALA* 5.0 1.8 - - + -
111D MET* 4.1 17.3 - - - -
114D TRP* 4.0 29.6 - - + -
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Residues in contact with LYS 40 (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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39D VAL* 1.3 73.5 - - - +
41D GLN* 1.3 65.3 + - - +
42D ARG* 3.6 24.2 + - - +
46D GLY 3.5 2.8 - - - +
47D LEU* 3.6 1.4 - - - -
48D GLU* 2.7 54.2 + - + +
50D ILE* 4.0 7.3 - - + +
66D PHE* 3.9 15.4 - - + -
91D GLU 2.7 30.9 + - - -
92D ASP* 3.8 11.7 + - - +
94D ALA* 3.9 11.2 - - + -
95D VAL 3.8 3.6 - - - -
96D TYR* 3.7 28.5 + - + +
705D GOL 3.3 30.8 + - - -
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Residues in contact with GLN 41 (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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44C GLN* 2.9 43.4 + - - +
93C TYR* 3.4 14.0 + - - -
40D LYS* 1.3 76.2 - - - +
42D ARG* 1.3 62.0 + - - +
43D PRO* 3.9 1.0 - - - +
44D GLU 6.0 0.2 - - - +
45D GLN 3.5 17.3 - - - +
46D GLY 3.8 4.5 - - - +
47D LEU* 3.5 15.4 - - + +
94D ALA* 3.5 3.4 - - - +
95D VAL* 2.8 44.1 + - + +
97D TYR* 3.3 25.0 + - + -
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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