Contacts of the strand formed by residues 37 - 48 (chain A) in PDB entry 4BNR
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 PHE 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY* 1.3 87.8 + - - -
38A SER* 1.3 73.9 + - - +
39A PHE* 4.8 8.5 - - + -
49J GLU* 4.3 25.6 - - - +
52J MET* 3.4 52.9 - - + +
53J ARG* 3.8 16.4 - - - +
56J GLY* 6.0 0.9 - - - -
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Residues in contact with SER 38 (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 GLN* 3.4 23.6 - - - -
35A GLU 3.3 10.5 - - - -
36A THR* 3.5 9.4 - - - +
37A PHE* 1.3 83.4 + - - +
39A PHE* 1.3 63.5 + - - +
40A HIS 4.3 0.4 + - - -
65A GLN* 3.5 16.0 + - - -
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Residues in contact with PHE 39 (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 GLN* 3.2 5.4 - - - -
35A GLU* 2.8 44.5 + - + +
37A PHE* 4.8 14.4 - - + -
38A SER* 1.3 78.1 - - - +
40A HIS* 1.3 77.1 + - - +
41A PHE* 3.5 8.3 + + + -
17I ARG* 3.1 46.0 - - - -
18I ILE* 5.0 0.2 - - - -
19I ILE* 3.5 37.0 - - + -
28J GLY 5.2 4.5 - - - -
29J LEU* 5.4 0.9 - - + -
52J MET* 5.3 16.6 - - + -
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Residues in contact with HIS 40 (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 SER* 2.7 29.1 + - - +
33A PHE 3.7 5.4 + - - -
34A GLN* 3.9 6.7 - - + +
38A SER 4.3 0.2 - - - -
39A PHE* 1.3 92.3 - - - +
41A PHE* 1.3 61.6 + - - +
42A CYS 3.0 25.9 + - - -
43A GLY* 4.2 2.9 - - - -
73A MET* 3.8 20.1 - - + +
141A TRP* 3.9 41.6 - + + +
151A THR* 6.0 0.7 - - + -
193A GLY* 2.8 29.7 + - - -
17I ARG* 4.1 7.5 - - - +
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Residues in contact with PHE 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 PHE* 3.2 52.7 + + - -
34A GLN 3.6 17.5 - - - -
35A GLU* 3.7 18.8 - - + -
39A PHE* 3.8 8.7 - + + -
40A HIS* 1.3 76.8 - - - +
42A CYS* 1.3 76.0 + - + +
58A CYS 3.3 23.6 - - - -
60A ASP* 5.8 0.7 - - - -
64A LEU* 4.0 14.6 - - + -
193A GLY* 4.0 2.6 - - - -
16I ALA* 3.4 1.4 - - - -
17I ARG* 2.8 47.2 + - - +
18I ILE* 4.5 16.2 - - + -
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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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33A PHE* 2.9 29.1 + - + -
40A HIS* 3.0 16.2 + - - -
41A PHE* 1.3 101.8 - - + +
43A GLY* 1.3 64.7 + - - +
58A CYS* 2.1 51.1 - - + -
193A GLY 3.9 5.8 - - - -
195A SER* 3.2 6.5 - - - +
16I ALA* 3.5 18.4 - - - -
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Residues in contact with GLY 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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30A GLN* 4.3 4.9 - - - -
31A LEU 3.5 11.0 - - - -
33A PHE* 4.0 2.6 - - - +
40A HIS* 4.4 4.3 - - - -
42A CYS* 1.3 76.7 - - - +
44A ALA* 1.3 61.8 + - - +
54A THR* 2.8 21.5 + - - -
193A GLY 3.9 5.1 + - - -
194A ASP* 4.1 2.4 + - - -
195A SER 2.7 13.3 + - - +
196A GLY 3.2 10.2 - - - -
197A GLY* 3.9 9.4 - - - -
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Residues in contact with ALA 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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29A TYR 3.9 0.2 - - - +
30A GLN* 3.9 6.6 + - - -
31A LEU* 2.9 47.5 + - + +
33A PHE* 4.6 6.3 - - + -
43A GLY* 1.3 76.3 - - - +
45A SER* 1.3 65.4 + - - +
52A ALA* 4.3 5.6 - - + -
53A ILE 3.3 16.2 - - - +
54A THR* 4.0 8.5 - - - -
66A ILE* 5.0 1.3 - - + -
106A LEU* 4.5 8.5 - - + -
196A GLY 3.4 5.6 + - - -
197A GLY* 3.9 2.7 - - - -
198A PRO* 4.1 1.6 - - - +
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Residues in contact with SER 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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29A TYR* 3.3 8.1 - - - -
31A LEU* 3.8 4.7 - - - -
44A ALA* 1.3 75.9 + - - +
46A ILE* 1.3 62.2 + - - +
52A ALA* 3.2 5.0 - - - -
53A ILE* 2.8 38.1 + - - +
121A ILE* 4.2 18.6 - - - -
196A GLY 4.5 0.5 + - - -
197A GLY 4.2 1.6 - - - -
198A PRO* 3.3 32.7 - - - +
209A LEU* 3.7 15.8 - - - +
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Residues in contact with ILE 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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28A PRO 3.6 23.3 - - - +
29A TYR* 3.0 8.5 + - - +
31A LEU* 3.5 34.3 - - + -
45A SER* 1.3 71.6 - - - +
47A TYR* 1.3 59.8 + - - +
48A ASN 3.5 20.6 - - - +
51A TYR 4.1 3.1 - - - -
53A ILE* 5.4 0.7 - - - -
68A ALA* 4.3 0.4 - - + -
112A LEU* 3.8 16.4 - - + -
114A PHE* 4.0 6.5 - - + -
118A VAL* 3.8 24.0 - - + -
119A ALA 3.7 11.7 - - - +
120A PRO* 3.4 17.2 - - + +
121A ILE* 3.1 31.3 + - - +
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Residues in contact with TYR 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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45A SER 3.4 1.8 + - - -
46A ILE* 1.3 73.4 - - - +
48A ASN* 1.3 86.1 + - + +
51A TYR* 3.0 17.6 + - + +
53A ILE* 3.8 24.0 - - + -
105A LEU* 5.4 0.7 - - + -
120A PRO* 3.5 14.1 - - - +
121A ILE 4.7 6.8 - - - +
123A LEU* 3.4 37.7 - - + -
239A ILE* 3.9 13.0 - - + -
240A LYS* 3.9 22.2 - - - +
243A ALA* 3.5 35.7 + - + -
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Residues in contact with ASN 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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46A ILE* 3.5 10.8 - - - +
47A TYR* 1.3 104.3 - - + +
49A GLU* 1.3 79.9 + - - +
50A ASN* 2.8 20.6 + - - +
51A TYR* 3.0 33.8 + - - +
112A LEU* 3.9 2.9 - - - +
114A PHE* 3.7 12.1 - - - -
120A PRO* 4.6 2.5 - - + -
243A ALA 4.4 5.3 + - - -
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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