Contacts of the strand formed by residues 40 - 48 (chain D) in PDB entry 3W58
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 ASN 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D GLY* 3.3 0.5 - - - -
36D LYS* 2.9 48.2 + - + +
37D ASP* 2.9 37.3 + - - +
38D SER 3.5 0.2 - - - -
39D ASN* 1.3 87.0 - - - +
41D LEU* 1.3 59.5 + - - +
42D CYS 4.0 0.2 + - - -
63D LYS 3.1 5.8 - - - -
64D ASP* 3.7 9.2 - - - +
65D GLY* 2.9 27.5 + - - +
112D LEU* 3.8 12.6 - - + +
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Residues in contact with LEU 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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33D ASN* 3.7 43.3 - - + +
34D LEU 3.3 15.0 - - - +
37D ASP 3.4 19.5 - - - +
38D SER 4.0 14.8 - - - +
40D ASN* 1.3 72.5 - - - +
42D CYS* 1.3 62.5 + - - +
43D LEU 4.2 7.9 - - - +
44D HIS* 4.5 2.2 - - + +
62D SER* 3.3 6.6 - - - -
63D LYS* 2.8 47.3 + - + +
68D TRP* 4.2 22.9 - - + -
112D LEU* 3.6 6.2 - - - +
119D TYR* 4.0 14.8 - - + -
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Residues in contact with CYS 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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34D LEU* 2.8 25.5 + - - -
35D GLY* 3.7 10.6 - - - -
41D LEU* 1.3 72.9 - - - +
43D LEU* 1.3 61.2 + - - +
61D ASN 4.4 1.6 - - - -
62D SER* 4.4 2.2 - - - -
96D LEU* 3.8 33.8 - - + +
108D PHE* 3.3 25.8 - - - -
109D PRO 4.7 1.9 - - - +
110D ASN* 4.7 4.7 - - - +
111D ARG* 5.9 1.7 + - - +
112D LEU* 3.9 9.7 - - + +
114D LEU* 3.7 23.6 - - + -
117D ILE* 3.8 18.8 - - - -
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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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32D LEU 3.5 1.2 - - - +
33D ASN* 3.3 4.0 - - - +
34D LEU* 2.8 56.8 + - + -
41D LEU* 3.2 3.4 - - - -
42D CYS* 1.3 80.7 - - - +
44D HIS* 1.4 64.5 + - - +
45D PHE* 4.1 19.5 - - + +
60D CYS* 4.1 26.9 - - + -
61D ASN 3.7 1.6 - - - -
89D ILE* 4.9 3.1 - - + -
96D LEU* 3.9 16.2 - - + -
98D VAL* 3.7 29.4 - - + -
108D PHE* 3.9 23.3 - - + -
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Residues in contact with HIS 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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31D VAL* 3.6 29.1 - - + +
33D ASN* 2.7 27.7 + - - +
41D LEU* 4.5 5.2 - - + +
43D LEU* 1.4 70.1 - - - +
45D PHE* 1.4 57.9 + - - +
46D ASN* 3.9 20.6 + - + +
59D VAL* 3.4 7.5 - - + +
60D CYS* 3.1 26.7 - - - -
61D ASN* 2.8 28.6 + - + +
68D TRP* 3.6 39.0 - + + -
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Residues in contact with PHE 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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30D PHE* 3.9 20.9 - + - -
31D VAL* 3.3 5.7 - - - -
32D LEU* 2.8 54.2 + - + +
43D LEU* 3.6 22.0 - - + -
44D HIS* 1.4 70.5 + - - +
46D ASN* 1.3 59.0 + - - +
47D PRO* 3.2 34.0 - - + +
58D ILE* 3.6 28.0 - - + -
59D VAL 4.1 0.9 - - - -
60D CYS* 4.1 9.4 - - - -
79D PHE* 4.4 3.4 - + - -
87D VAL* 4.4 12.8 - - + -
98D VAL* 4.3 7.0 - - + -
100D LEU* 4.0 26.9 - - + -
106D PHE* 4.0 18.6 - + - -
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Residues in contact with ASN 46 (chain D).
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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29D SER* 4.2 11.1 + - - -
30D PHE 3.0 15.1 + - - -
31D VAL* 3.6 15.0 - - + +
44D HIS* 3.9 21.3 + - - +
45D PHE* 1.3 75.7 - - - +
47D PRO* 1.3 66.8 + - - +
48D ARG* 3.1 34.9 + - - +
58D ILE* 4.3 0.7 - - - -
59D VAL* 2.8 41.4 + - + +
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Residues in contact with PRO 47 (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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29D SER* 2.9 26.2 - - - -
30D PHE* 3.1 29.3 + - + +
45D PHE* 3.2 45.1 - - + +
46D ASN* 1.3 88.2 - - - +
48D ARG* 1.3 60.4 + - - +
49D PHE* 4.0 4.5 - - + -
57D THR 3.9 4.9 - - - +
58D ILE* 3.9 12.8 - - + -
77D PHE 5.5 0.4 - - - +
79D PHE* 3.6 28.9 - - + -
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Residues in contact with ARG 48 (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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28D LYS 3.4 7.2 - - - +
29D SER* 3.8 10.1 - - - -
46D ASN* 3.1 28.8 + - - +
47D PRO* 1.3 80.3 - - - +
49D PHE* 1.3 65.0 + - - +
55D ALA* 3.5 20.6 - - + +
56D ASN* 3.4 2.6 - - - -
57D THR* 2.8 46.5 + - - +
58D ILE* 4.9 0.5 - - - +
59D VAL* 3.5 31.3 - - - +
71D GLU* 5.5 1.8 + - - -
76D VAL* 3.7 5.7 - - - +
77D PHE 4.8 0.5 + - - +
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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