Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 6BM0
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLN* 5.9 0.2 - - - -
10A PRO* 4.2 12.9 - - - +
11A PRO* 3.3 33.8 - - + +
33A ALA* 3.5 3.3 - - - +
34A GLY* 3.0 28.0 + - - +
35A THR 3.3 6.9 + - - +
36A SER* 1.3 82.0 - - - +
38A LEU* 1.3 60.8 + - - +
39A TYR* 3.0 44.6 + - + +
71A SER* 5.1 4.4 + - - -
72A PHE 3.3 18.1 + - - +
73A SER* 4.4 10.0 - - - -
74A PHE* 4.4 5.1 - - - +
78A VAL* 4.9 1.4 - - - +
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Residues in contact with LEU 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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22A PHE* 4.8 4.0 - - + -
31A VAL* 3.8 19.7 - - + -
32A VAL 3.4 16.6 - - - +
33A ALA* 3.7 15.7 - - + -
37A GLN* 1.3 71.7 - - - +
39A TYR* 1.3 69.9 + - - +
40A VAL* 4.9 1.6 - - + -
70A ALA 4.1 0.7 - - - +
71A SER* 3.4 0.7 - - - -
72A PHE* 2.7 51.9 + - + +
74A PHE* 3.9 33.8 - - + -
78A VAL* 6.3 0.2 - - + -
81A MET* 3.9 9.2 - - - -
94A LEU* 4.0 21.5 - - + -
96A LEU* 5.0 4.0 - - + -
115A LEU* 4.1 15.7 - - + -
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Residues in contact with TYR 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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10A PRO* 5.0 4.9 - - - +
11A PRO 3.8 12.8 + - - -
12A THR* 5.4 7.7 - - + +
14A LEU* 3.9 27.6 - - + -
31A VAL* 3.6 4.0 - - - +
32A VAL* 2.9 45.5 + - + +
37A GLN* 3.0 50.4 + - + -
38A LEU* 1.3 83.9 - - - +
40A VAL* 1.3 64.1 + - - +
41A TYR* 3.9 24.9 - + + -
68A LEU* 4.5 8.1 - - + -
70A ALA 3.6 3.1 - - - -
71A SER* 3.7 20.9 - - - -
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Residues in contact with VAL 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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22A PHE* 3.7 48.7 - - + -
23A PHE* 4.3 9.4 - - + -
29A ASN* 3.8 30.7 - - + +
30A LEU 3.5 3.6 - - - +
31A VAL* 4.4 10.5 - - + -
38A LEU* 4.9 4.9 - - + -
39A TYR* 1.3 76.9 - - - +
41A TYR* 1.3 61.5 + - - +
68A LEU* 3.5 3.5 - - - +
69A ALA* 2.9 28.1 + - + +
70A ALA* 2.8 25.0 + - + +
72A PHE* 4.9 2.9 - - + -
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Residues in contact with TYR 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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14A LEU* 4.9 0.9 - - + +
29A ASN* 3.5 8.3 - - - -
30A LEU* 2.7 67.0 + - + +
32A VAL* 3.7 24.0 - - + -
39A TYR* 3.9 21.1 - - + -
40A VAL* 1.3 74.3 - - - +
42A ARG* 1.3 67.0 + - - +
66A LEU* 4.4 10.1 - - + -
67A GLU 3.3 4.7 - - - +
68A LEU* 3.5 44.5 - - + +
469A ILE* 3.5 40.3 - - + +
958A ARG* 4.8 10.2 - - - -
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Residues in contact with ARG 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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23A PHE* 3.4 27.6 - - + -
27A GLU* 3.9 24.4 + - - +
28A ARG 5.1 3.4 - - - +
29A ASN* 3.3 20.0 - - - +
40A VAL 4.2 0.8 + - - -
41A TYR* 1.3 75.4 - - - +
43A LEU* 1.3 67.4 + - - +
44A ASN* 5.5 3.1 + - - +
66A LEU* 3.6 12.0 - - - +
67A GLU* 2.8 45.9 + - + +
69A ALA* 3.4 16.9 - - + +
860A ARG* 3.3 29.7 - - - +
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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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42A ARG* 1.3 80.5 - - - +
44A ASN* 1.3 77.3 + - - +
45A ARG* 4.9 18.0 + - + +
64A GLU* 4.0 10.5 - - + -
66A LEU* 3.8 28.3 - - + +
67A GLU* 4.7 2.0 - - - +
377A MET* 4.6 16.8 - - - -
378A GLU* 3.9 28.5 - - - +
381A TYR* 4.7 13.7 - - + -
393A LEU* 3.9 20.9 - - + -
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Residues in contact with ASN 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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42A ARG* 5.5 3.3 + - - +
43A LEU* 1.3 80.3 + - - +
45A ARG* 1.3 69.7 + - - +
64A GLU* 3.4 24.1 - - - +
65A LYS* 3.5 16.2 + - + +
67A GLU* 2.4 42.4 + - - +
856A SER* 5.4 9.9 - - - -
957A GLY 5.1 2.8 + - - -
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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