Contacts of the strand formed by residues 29 - 34 (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 ASN 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.6 5.6 - - - -
20A CYS 2.9 36.0 + - - +
22A PHE* 3.8 11.0 - - + +
23A PHE* 3.5 45.2 - - - +
27A GLU* 4.4 8.7 + - - +
28A ARG* 1.3 84.0 - - - +
30A LEU* 1.3 62.5 + - - +
31A VAL* 3.5 3.7 + - + +
40A VAL* 3.8 18.4 - - + +
41A TYR 3.5 8.0 - - - +
42A ARG* 3.3 28.0 - - - +
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Residues in contact with LEU 30 (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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17A SER* 4.5 2.2 - - - -
18A MET 3.3 20.4 - - - +
19A TYR* 4.4 4.2 - - - -
29A ASN* 1.3 70.1 - - - +
31A VAL* 1.3 59.9 + - - +
32A VAL* 3.7 19.7 + - + -
39A TYR 4.0 0.2 - - - +
40A VAL* 3.5 1.7 - - - -
41A TYR* 2.7 67.8 + - + +
66A LEU* 3.9 13.9 - - + -
375A VAL* 4.5 7.9 - - + -
377A MET* 4.1 17.9 - - + -
383A PHE* 3.6 46.2 - - + -
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Residues in contact with VAL 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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17A SER* 3.4 2.3 - - - -
18A MET* 2.9 45.5 + - + +
20A CYS* 3.8 23.8 - - - -
22A PHE* 4.3 21.1 - - + -
29A ASN 3.8 6.7 - - - +
30A LEU* 1.3 75.0 - - - +
32A VAL* 1.3 61.7 + - - +
38A LEU* 3.8 26.0 - - + -
39A TYR 3.6 5.8 - - - +
40A VAL* 4.4 9.2 - - + -
81A MET* 3.6 8.1 - - + +
94A LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 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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14A LEU* 3.7 26.0 - - + -
16A PHE 3.3 7.6 - - - +
17A SER* 3.7 12.1 - - - -
30A LEU* 3.7 15.5 - - + -
31A VAL* 1.3 77.1 - - - +
33A ALA* 1.3 61.4 + - - +
38A LEU* 3.4 5.0 - - - +
39A TYR* 2.9 52.1 + - + +
41A TYR* 3.7 14.4 - - + -
383A PHE* 3.6 31.2 - - + -
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Residues in contact with ALA 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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14A LEU* 4.3 4.0 - - - -
15A GLU* 3.0 6.1 + - - +
16A PHE* 2.9 38.2 + - + +
32A VAL* 1.3 76.9 - - - +
34A GLY* 1.3 63.4 + - - +
37A GLN 3.5 7.9 - - - +
38A LEU* 3.7 8.7 - - + -
78A VAL* 4.6 15.3 - - + -
81A MET* 3.7 29.2 - - + -
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Residues in contact with GLY 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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13A GLY 3.7 18.4 - - - -
14A LEU* 4.2 7.2 - - - +
15A GLU* 4.0 13.8 - - - +
16A PHE* 5.5 0.7 - - - -
33A ALA* 1.3 75.2 - - - +
35A THR* 1.3 62.5 + - - -
36A SER 3.0 8.5 + - - -
37A GLN* 3.0 14.4 + - - +
78A VAL* 4.0 18.9 + - - +
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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