Contacts of the strand formed by residues 40 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLY* 3.3 1.0 - - - -
36A LYS* 2.9 49.8 + - + +
37A ASP* 3.0 36.0 + - - +
38A SER 3.4 0.2 - - - -
39A ASN* 1.3 88.3 - - - +
41A LEU* 1.3 59.8 + - - +
63A LYS 3.2 4.9 - - - -
64A ASP* 3.7 8.5 - - - +
65A GLY* 2.8 27.4 + - - +
112A LEU* 3.7 12.6 - - + +
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Residues in contact with LEU 41 (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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33A ASN* 3.6 42.4 - - + +
34A LEU 3.2 14.6 - - - +
37A ASP 3.4 20.2 - - - +
38A SER* 4.1 15.3 - - - +
40A ASN* 1.3 74.3 - - - +
42A CYS* 1.3 63.4 + - - +
43A LEU 4.2 8.3 - - - +
44A HIS* 4.5 3.1 - - + +
62A SER* 3.5 5.2 - - - -
63A LYS* 2.8 53.2 + - + +
68A TRP* 4.4 14.4 - - + -
112A LEU* 3.6 5.5 - - - +
119A TYR* 3.9 14.4 - - + -
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Residues in contact with CYS 42 (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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34A LEU* 2.9 26.3 + - - -
35A GLY* 3.8 10.4 - - - -
40A ASN 4.0 0.6 + - - -
41A LEU* 1.3 73.7 - - - +
43A LEU* 1.3 62.1 + - - +
61A ASN 4.5 1.6 - - - -
62A SER* 4.3 1.6 - - - -
96A LEU* 3.8 32.4 - - + +
108A PHE* 3.5 24.3 - - - -
109A PRO 4.6 3.1 - - - +
110A ASN* 4.5 6.7 - - - +
111A ARG 5.7 1.1 + - - +
112A LEU* 4.0 12.1 - - + +
114A LEU* 3.6 24.7 - - + -
117A ILE* 3.9 15.7 - - - -
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Residues in contact with LEU 43 (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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32A LEU* 3.6 2.4 - - + +
33A ASN* 3.3 5.0 - - - +
34A LEU* 2.8 52.3 + - + +
41A LEU* 3.2 3.9 - - - +
42A CYS* 1.3 82.0 - - - +
44A HIS* 1.3 71.9 + - - +
45A PHE* 4.1 20.4 - - + -
60A CYS* 4.1 20.0 - - + -
61A ASN 3.7 1.8 - - - +
89A ILE* 4.8 4.7 - - + -
96A LEU* 3.8 18.2 - - + -
98A VAL* 3.7 27.8 - - + -
108A PHE* 4.0 26.0 - - + -
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Residues in contact with HIS 44 (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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31A VAL* 3.5 28.4 - - + +
33A ASN* 2.7 27.3 + - - +
41A LEU* 4.5 4.2 - - + +
43A LEU* 1.3 71.8 - - - +
45A PHE* 1.4 58.4 + - - +
46A ASN* 3.9 20.2 + - + +
48A ARG* 5.9 1.0 + - - -
59A VAL* 3.5 6.4 - - + +
60A CYS* 3.1 10.6 - - - +
61A ASN* 2.7 45.9 + - + +
68A TRP* 3.6 39.4 - + + -
71A GLU* 6.0 1.1 - - - -
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Residues in contact with PHE 45 (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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30A PHE* 4.3 6.5 - + - -
31A VAL* 3.2 6.0 - - - -
32A LEU* 2.9 57.7 + - + +
43A LEU* 4.1 16.8 - - + -
44A HIS* 1.4 72.2 - - - +
46A ASN* 1.3 58.8 + - - +
47A PRO* 3.4 27.9 - - + +
58A ILE* 3.6 16.8 - - + -
59A VAL 4.0 1.1 - - - -
60A CYS* 3.9 17.3 - - - -
79A PHE* 3.8 7.6 - + - -
87A VAL* 4.1 20.0 - - + -
98A VAL* 4.2 7.6 - - + -
100A LEU* 3.5 32.5 - - + -
106A PHE* 4.0 13.5 - + - -
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Residues in contact with ASN 46 (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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29A SER* 4.0 8.5 + - - -
30A PHE 3.0 15.5 + - - -
31A VAL* 3.5 14.3 - - + +
44A HIS* 3.9 21.2 + - + +
45A PHE* 1.3 76.5 - - - +
47A PRO* 1.3 69.0 + - - +
48A ARG* 2.8 43.1 + - - +
52A HIS* 5.3 0.9 - - - -
57A THR 3.6 0.5 - - - +
58A ILE* 4.4 0.7 - - - -
59A VAL* 2.8 41.2 + - + +
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Residues in contact with PRO 47 (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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29A SER* 3.3 5.0 - - - -
30A PHE* 3.1 66.5 + - + +
45A PHE* 3.4 38.1 - - + +
46A ASN* 1.3 85.1 - - - +
48A ARG* 1.3 59.2 + - - +
49A PHE* 4.1 1.9 - - + -
57A THR 3.8 5.4 - - - +
58A ILE* 4.1 6.5 - - + -
77A PHE* 3.8 18.8 - - + -
79A PHE* 3.9 11.9 - - + -
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Residues in contact with ARG 48 (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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28A LYS 3.9 3.4 - - - -
29A SER* 3.9 7.6 - - - -
44A HIS* 5.9 1.2 + - - -
46A ASN* 2.8 36.5 + - - +
47A PRO* 1.3 72.5 - - - +
49A PHE* 1.3 60.8 + - - +
51A ALA* 3.9 17.7 - - + -
52A HIS* 3.5 35.2 + - - +
54A ASP* 2.9 34.1 + - - +
56A ASN* 2.9 21.0 + - - -
57A THR* 2.7 29.6 + - - +
59A VAL* 3.8 22.5 - - - +
71A GLU* 4.5 12.5 + - - -
77A PHE* 3.4 3.4 - - - -
203A GOL 3.8 12.9 + - - -
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Residues in contact with PHE 49 (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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23A VAL* 3.6 30.5 - - + -
27A ALA* 3.6 24.0 - - + +
28A LYS 2.7 24.8 + - - +
29A SER* 3.9 2.9 - - - -
30A PHE* 3.9 21.1 - + - -
47A PRO 4.5 1.8 - - - -
48A ARG* 1.3 73.2 - - - +
50A ASN* 1.3 61.0 + - + +
54A ASP 3.9 0.2 - - - -
55A ALA* 3.1 8.8 - - - +
56A ASN* 3.0 30.3 + - - +
77A PHE* 3.6 26.2 - + - -
79A PHE* 3.9 20.2 - - + -
80A GLN 3.8 21.1 - - - -
81A PRO* 3.9 16.6 - - + -
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Residues in contact with ASN 50 (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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28A LYS* 2.7 63.3 + - + +
49A PHE* 1.3 81.2 - - + +
51A ALA* 1.3 60.5 + - - +
53A GLY* 5.1 4.9 + - - -
54A ASP 3.1 12.2 + - - +
55A ALA* 5.2 4.1 - - + +
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Residues in contact with ALA 51 (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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28A LYS* 4.0 9.4 - - + +
29A SER* 3.9 28.3 - - - +
48A ARG* 3.9 11.3 - - + +
50A ASN* 1.3 78.4 + - - +
52A HIS* 1.3 85.9 + - + +
53A GLY 3.1 2.5 - - - -
54A ASP* 2.9 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