Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 4D9R
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 MET 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D VAL* 4.5 3.8 - - + -
23D CYS* 4.2 13.2 - - + -
25D THR* 3.7 29.8 - - + -
29D ILE* 4.0 5.8 - - + -
31D ASP 2.8 7.0 + - - +
32D ASP* 1.4 73.2 - - - +
34D ASN* 1.3 68.5 + - - +
35D TRP* 3.9 16.2 - - + +
48D ILE* 4.2 3.6 - - - +
49D SER 3.4 5.5 - - - +
50D GLY* 3.3 20.3 + - - -
51D GLY 4.8 0.3 + - - -
52D ASN* 4.9 6.5 - - - +
71D PHE* 3.4 53.2 - - + -
88D CYS* 3.7 11.4 - - - -
89D LEU 3.3 20.4 - - - +
90D GLN* 4.1 7.9 - - + +
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Residues in contact with ASN 34 (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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170B ARG* 3.5 24.5 - - - +
32D ASP 4.4 0.2 - - - -
33D MET* 1.3 76.6 - - - +
35D TRP* 1.3 66.5 + - - +
36D TYR* 4.5 0.4 - - + -
46D LEU* 3.7 12.2 - - + +
48D ILE 3.1 8.3 - - - +
49D SER* 3.4 21.7 - - - -
50D GLY 3.7 4.1 + - - -
88D CYS* 3.1 7.1 - - - +
89D LEU* 2.7 61.6 + - + +
91D SER* 2.9 32.6 + - - +
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Residues in contact with TRP 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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6D GLN* 4.0 5.4 - - - -
21D ILE* 3.7 37.7 - - + -
22D THR 4.0 1.6 - - - -
23D CYS* 3.8 15.5 - - + -
33D MET* 3.9 12.5 - - + +
34D ASN* 1.3 79.2 - - - +
36D TYR* 1.3 57.3 + - - +
46D LEU* 3.6 4.3 - - - +
47D LEU* 2.7 34.5 + - + -
48D ILE* 2.9 35.2 + - + -
52D ASN* 4.8 6.6 + - - -
64D GLY* 5.0 1.6 - - - -
71D PHE* 4.1 16.4 - - + +
72D THR 3.9 14.6 + - - -
73D LEU* 3.5 54.1 - - + -
86D TYR 5.5 0.2 - - - -
87D TYR 3.4 10.1 - - - -
88D CYS* 3.5 37.2 - - + -
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Residues in contact with TYR 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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170B ARG* 2.9 19.6 - - - -
34D ASN* 4.5 0.7 - - + -
35D TRP* 1.3 78.9 - - - +
37D GLN* 1.3 60.5 + - - +
44D PRO* 4.1 19.1 - - + -
45D LYS 3.2 7.0 - - - -
46D LEU* 3.6 39.7 - - + -
47D LEU* 4.3 4.5 - - - -
85D THR 4.0 0.2 - - - +
86D TYR* 3.3 8.0 - - - +
87D TYR* 2.7 51.3 + - + +
89D LEU* 3.7 30.7 - - + +
98D PHE* 3.7 21.5 - + + -
97E GLU* 2.6 32.0 + - - -
111E TRP* 3.8 18.2 - + - -
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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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36D TYR* 1.3 75.1 - - - +
38D GLN* 1.3 62.8 + - - +
39D LYS* 3.4 35.1 + - - +
43D VAL 4.3 0.5 - - - +
44D PRO* 3.5 2.0 - - - +
45D LYS* 2.8 47.7 + - + +
47D LEU* 3.8 23.8 - - + +
62D PHE* 4.0 9.7 - - - -
81D GLU 4.4 0.2 - - - +
82D ASP* 4.2 7.4 - - - +
84D ALA* 3.8 11.4 - - + -
85D THR 3.8 3.4 - - - -
86D TYR* 2.9 39.1 + - + -
87D TYR* 5.5 0.2 - - - -
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Residues in contact with GLN 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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37D GLN* 1.3 74.0 - - - +
39D LYS* 1.3 70.4 + - - +
40D PRO 5.8 1.3 + - - -
42D LYS 3.1 22.6 + - - +
43D VAL 4.9 0.9 - - - -
44D PRO* 3.8 26.6 - - + +
84D ALA* 3.6 4.3 - - - -
85D THR* 2.8 42.7 + - - +
87D TYR* 3.6 20.7 + - + -
39E GLN* 3.0 40.7 + - - -
45E LEU* 3.9 2.0 - - - +
95E TYR* 3.7 9.1 + - - -
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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