Contacts of the strand formed by residues 40 - 46 (chain D) in PDB entry 3ZO7
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 TRP 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ARG* 4.2 0.5 + - - -
7D MET* 3.8 24.5 - - + -
31D SER* 3.6 32.3 - - - -
34D LEU* 3.0 30.2 + - + -
35D GLN* 3.4 37.2 - - + +
38D GLY 4.3 1.6 - - - -
39D GLN* 1.3 73.8 - - - +
41D ARG* 1.3 64.6 + - - +
42D TYR 3.3 18.3 + - - -
43D LEU* 3.8 27.6 - - + +
52D ASN* 4.5 4.0 - - - -
54D SER* 2.9 29.7 + - - -
55D VAL 4.3 1.1 - - - -
56D PHE* 3.4 25.4 - + + -
71D LEU* 3.9 25.8 - - + -
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Residues in contact with ARG 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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44A TRP* 6.2 1.5 - - - +
90A ARG* 3.2 16.2 + - - -
2D LEU* 4.2 21.2 - - - +
38D GLY* 4.2 14.4 - - - +
39D GLN 3.4 2.0 + - - -
40D TRP* 1.3 74.9 - - - +
42D TYR* 1.3 109.9 + - + +
55D VAL* 2.9 20.2 + - + +
57D ASP* 3.9 29.9 + - + -
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Residues in contact with TYR 42 (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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41A ARG* 6.3 0.2 - - - -
42A TYR* 3.3 39.1 + + - -
44A TRP* 4.0 20.4 - + - -
90A ARG* 3.8 15.5 - - - +
40D TRP* 3.3 11.2 - - - -
41D ARG* 1.3 132.0 + - + +
43D LEU* 1.3 61.5 + - - +
44D TRP* 3.6 34.1 - + + -
53D ILE 4.5 0.4 - - - -
54D SER* 3.3 5.6 - - - -
55D VAL* 3.1 45.1 + - + -
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Residues in contact with LEU 43 (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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87A HIS* 3.4 39.1 + - + +
89A ALA* 3.9 13.5 - - + +
90A ARG* 3.8 28.7 + - - +
31D SER* 5.0 1.8 - - - +
35D GLN* 3.8 25.6 - - - +
40D TRP* 3.8 22.2 - - + +
42D TYR* 1.3 75.9 - - - +
44D TRP* 1.3 73.0 + - - +
52D ASN* 3.6 28.7 - - + +
53D ILE 3.6 2.2 - - - -
54D SER* 3.4 18.6 - - - +
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Residues in contact with TRP 44 (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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2A LEU* 3.5 30.2 - - + +
4A LEU* 5.4 1.3 - - + -
41A ARG* 4.5 5.8 - - - +
42A TYR* 3.9 22.7 - + - -
44A TRP* 4.6 1.3 - + - -
55A VAL* 3.9 27.6 - - + -
84A LEU* 3.8 33.9 - - + -
85A SER 3.7 11.4 - - - +
86A HIS* 5.6 2.5 - - - -
87A HIS* 4.0 7.0 - - - +
90A ARG* 6.1 0.6 - - - +
4D LEU* 5.6 0.4 - - + -
42D TYR* 3.6 39.7 - + + -
43D LEU* 1.3 81.2 + - - +
45D ARG* 1.3 59.3 + - - +
52D ASN* 3.1 8.7 - - - +
53D ILE* 2.9 58.6 + - + +
55D VAL* 4.2 14.8 - - + -
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Residues in contact with ARG 45 (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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84A LEU* 3.6 5.9 - - - +
85A SER* 2.7 50.5 + - - +
86A HIS 3.7 15.0 - - - +
87A HIS* 3.1 32.1 + - - +
88A PRO* 3.6 28.1 - - - +
65B HIS* 3.3 44.5 + - + +
69B TRP* 5.0 7.3 - - - -
44D TRP* 1.3 73.2 - - - +
46D THR* 1.3 64.1 + - - +
47D THR 3.2 0.7 + - - -
49D LYS 3.4 8.7 - - - -
50D TYR* 4.0 22.5 - - - -
51D GLY* 2.8 43.0 + - - +
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Residues in contact with THR 46 (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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82A GLU* 4.2 5.8 - - - +
83A PRO 4.8 3.1 - - - -
84A LEU* 5.2 1.6 - - - -
6D ARG* 4.0 17.9 - - + +
7D MET 5.3 0.7 - - - +
44D TRP 3.7 0.2 + - - -
45D ARG* 1.3 73.3 - - - +
47D THR* 1.3 66.6 + - - +
48D GLY 3.3 0.3 + - - -
49D LYS* 3.0 36.2 + - - +
51D GLY* 3.3 25.7 + - - -
52D ASN* 3.8 25.8 - - - +
53D ILE* 3.9 16.4 - - + -
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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