Contacts of the strand formed by residues 38 - 43 (chain A) in PDB entry 1MQ0
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 VAL 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LYS* 3.9 6.4 - - - +
29A ALA* 4.1 0.6 - - - +
36A PHE* 3.6 32.5 - - + +
37A PRO* 1.3 82.3 - - - +
39A GLY* 1.3 61.8 + - - +
53A CYS* 3.2 19.9 - - - +
54A ASN* 2.7 23.3 + - - +
66A ALA* 3.6 11.2 - - + -
87A ILE* 3.8 15.9 - - + -
88A ALA 3.2 13.2 - - - +
89A SER* 4.7 1.1 - - - -
96A ILE* 5.0 1.8 - - + -
148A BRD 3.5 42.6 - - - +
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Residues in contact with GLY 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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22A SER* 3.4 22.4 - - - -
26A LYS* 3.6 12.4 - - - +
38A VAL* 1.3 75.2 - - - +
40A ALA* 1.3 60.8 + - - +
52A GLY 3.3 7.0 - - - -
66A ALA* 3.8 2.2 - - - -
87A ILE* 3.4 8.1 - - - +
88A ALA 2.9 31.9 + - - -
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Residues in contact with ALA 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 SER* 4.0 2.9 - - - -
25A ALA* 3.5 5.4 - - - +
39A GLY* 1.3 74.2 - - - +
41A ALA* 1.3 61.8 + - - +
50A PHE 4.1 0.9 - - - -
51A LYS* 3.1 6.6 - - - -
52A GLY 2.7 33.3 + - - +
66A ALA* 3.4 32.3 - - + +
67A GLU* 3.8 14.8 - - + +
70A ALA* 3.8 7.2 - - + -
85A ILE* 4.3 7.0 - - + -
86A ALA 3.2 8.7 - - - +
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Residues in contact with ALA 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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18A LEU* 3.7 23.2 - - + +
21A CYS* 3.9 13.9 - - + -
22A SER* 3.5 29.8 - - - +
40A ALA* 1.3 73.8 - - - +
42A LEU* 1.3 62.2 + - - +
49A ILE* 4.1 4.7 - - + -
50A PHE 3.4 5.4 - - - -
51A LYS* 5.2 0.2 - - - -
85A ILE* 3.2 4.9 - - - -
86A ALA 3.0 28.6 + - - +
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Residues in contact with LEU 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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40A ALA 4.1 0.4 - - - -
41A ALA* 1.3 72.7 - - - +
43A LEU* 1.3 67.9 + - - +
44A THR* 3.7 0.8 + - + +
48A ARG 3.5 1.2 - - - +
49A ILE* 3.2 5.1 - - - -
50A PHE* 2.8 47.8 + - + +
70A ALA* 4.2 7.6 - - + +
71A ILE* 3.6 39.3 - - + -
74A ALA* 3.9 8.5 - - + -
82A PHE* 3.4 55.2 - - + -
84A ALA 3.4 12.6 - - - +
85A ILE* 4.3 11.2 - - + -
113A TRP* 4.1 4.0 - - + -
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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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13A GLU* 3.6 28.0 - - - +
14A CYS 4.3 5.6 - - - +
18A LEU* 3.8 21.8 - - + -
41A ALA 3.8 1.2 + - - -
42A LEU* 1.3 73.5 - - - +
44A THR* 1.3 79.4 + - - +
47A GLY* 3.6 28.5 - - - +
48A ARG 3.6 2.9 - - - +
49A ILE* 4.2 12.1 - - + -
82A PHE* 3.4 3.5 - - - -
83A ARG* 2.6 35.8 + - - -
84A ALA* 2.8 28.3 + - + +
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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