Contacts of the strand formed by residues 30 - 37 (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 GLN 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.0 20.0 + - + +
28A PRO 4.4 3.5 - - - +
29A TYR* 1.3 82.9 - - + +
31A LEU* 1.3 87.5 + - - +
43A GLY* 4.3 9.3 - - - -
44A ALA 4.0 3.2 + - - -
67A VAL 4.2 2.9 - - - +
68A ALA* 4.4 5.2 - - - -
69A GLY 4.5 4.0 + - - -
70A GLU 5.3 2.8 + - - +
139A THR* 2.7 37.0 + - - +
140A GLY* 4.1 4.9 - - - -
141A TRP* 3.6 27.9 - - + -
155A LEU* 3.8 24.7 - - + -
197A GLY* 4.6 0.2 - - - -
198A PRO* 3.2 21.9 - - - +
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Residues in contact with LEU 31 (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 4.0 1.1 - - - +
30A GLN* 1.3 94.7 + - - +
32A SER* 1.3 62.3 + - - +
43A GLY* 3.5 2.6 - - - -
44A ALA* 2.9 36.8 + - + +
45A SER 3.8 5.8 - - - -
46A ILE* 3.5 29.6 - - + -
52A ALA* 3.4 32.8 - - + -
66A ILE* 4.0 20.4 - - + -
67A VAL 3.4 5.2 - - - +
68A ALA* 3.4 37.5 - - + +
108A LEU* 6.0 0.2 - - + -
112A LEU* 5.5 1.8 - - + -
141A TRP* 3.8 5.7 - - - -
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Residues in contact with SER 32 (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 LEU* 1.3 72.4 - - - +
33A PHE* 1.3 59.4 + - - +
34A GLN* 2.9 32.3 + - - +
40A HIS* 2.7 28.6 + - - -
42A CYS 4.1 0.4 - - - -
66A ILE* 3.2 6.3 - - - -
67A VAL* 2.9 38.6 + - - -
70A GLU* 5.1 1.6 - - - -
73A MET* 3.3 13.2 - - - +
141A TRP* 3.8 10.9 - - - -
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Residues in contact with PHE 33 (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 LEU 4.0 1.0 - - - -
32A SER* 1.3 71.2 + - - +
34A GLN* 1.3 59.4 + - - +
40A HIS* 3.7 1.7 - - - -
41A PHE* 3.2 59.3 + + - -
42A CYS* 2.9 24.8 + - + +
43A GLY 4.0 8.1 - - - +
44A ALA* 4.6 4.0 - - + -
54A THR* 4.0 18.4 - - + -
58A CYS* 4.3 1.8 - - + -
59A VAL* 3.7 26.0 - - + -
60A ASP* 5.2 0.2 - - - -
64A LEU* 4.2 22.7 - - + -
65A GLN 3.5 15.5 - - - -
66A ILE* 4.2 2.7 - - + -
85A VAL* 4.2 12.8 - - + -
106A LEU* 3.7 37.5 - - + -
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Residues in contact with GLN 34 (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* 2.9 33.0 + - - +
33A PHE* 1.3 75.5 - - - +
35A GLU* 1.3 61.3 + - - +
38A SER* 3.4 14.2 - - - -
39A PHE 3.2 12.3 - - - +
40A HIS* 3.9 11.3 - - - +
41A PHE* 3.6 5.3 - - - -
64A LEU* 3.5 5.7 - - - +
65A GLN* 2.9 63.9 + - + +
67A VAL* 3.5 23.5 - - + +
70A GLU* 5.3 3.2 + - - -
73A MET* 4.0 14.3 - - - +
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Residues in contact with GLU 35 (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* 1.3 73.2 - - - +
36A THR* 1.3 64.8 + - - +
37A PHE* 3.3 39.0 - - + -
38A SER* 3.3 1.6 - - - -
39A PHE* 2.8 43.1 + - + +
41A PHE* 3.7 10.4 - - + -
62A SER 5.1 4.8 - - - +
63A GLY* 3.2 12.6 - - - +
64A LEU* 4.2 13.8 - - + +
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Residues in contact with THR 36 (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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35A GLU* 1.3 73.9 - - - +
37A PHE* 1.3 80.7 + - - +
38A SER* 3.5 11.7 - - - +
63A GLY* 2.8 37.4 + - - +
64A LEU 5.2 0.2 - - - -
65A GLN* 3.0 50.0 - - + +
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Residues in contact with PHE 37 (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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35A GLU* 3.3 51.1 - - + -
36A THR* 1.3 82.3 - - - +
37A ILE* 1.3 67.4 - - - +
38A SER* 5.3 0.2 + - - -
39A PHE* 5.1 4.3 - - + -
49J GLU* 6.1 3.1 - - + -
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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