Contacts of the strand formed by residues 41 - 46 (chain P) in PDB entry 2IMW
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 GLY 41 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32P VAL 3.1 13.7 - - - -
34P SER* 3.1 15.5 + - - -
39P ASP 4.0 0.9 - - - +
40P SER* 1.3 76.6 - - - +
42P ALA* 1.3 61.0 + - - -
60P PRO* 3.6 7.3 - - - +
61P ILE* 3.0 26.6 + - - +
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Residues in contact with ALA 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P CYS* 3.6 0.9 - - - -
32P VAL* 2.9 36.1 + - + +
41P GLY* 1.3 76.1 - - - -
43P VAL* 1.3 67.3 - - - +
44P ALA 3.4 0.2 + - - -
58P GLY 4.2 13.5 - - - +
59P ILE 3.4 11.7 - - - +
60P PRO* 4.8 1.3 - - + -
61P ILE* 3.8 5.7 - - - +
401P DDS 4.5 13.0 - - + +
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Residues in contact with VAL 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P VAL* 3.6 26.7 - - + -
30P VAL 3.8 3.1 - - - -
31P CYS* 4.4 1.8 - - - +
42P ALA* 1.3 71.8 - - - +
44P ALA* 1.3 60.2 + - - +
45P THR 3.6 26.0 - - - +
46P ALA 4.5 0.2 - - - +
55P VAL* 4.3 2.9 - - + -
56P LYS* 3.5 29.6 - - - +
58P GLY* 2.8 28.1 + - - -
59P ILE* 2.9 30.4 + - + +
61P ILE* 4.1 8.9 - - + +
64P ALA* 4.0 13.9 - - + -
401P DDS 4.0 6.5 + - - -
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Residues in contact with ALA 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P TYR* 4.5 2.2 - - + -
30P VAL* 2.8 18.8 + - + +
32P VAL* 4.0 6.3 - - + -
42P ALA 3.4 3.2 + - - -
43P VAL* 1.3 73.8 - - - +
45P THR* 1.3 65.6 + - - +
57P ALA* 3.1 19.6 - - - +
76P MET* 2.7 39.7 - - + -
401P DDS 3.5 29.2 + - + +
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Residues in contact with THR 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR* 4.6 1.6 - - - +
12P TYR* 3.6 37.2 - - + +
13P ALA* 3.9 12.3 - - + +
30P VAL* 2.8 31.8 + - + +
43P VAL* 3.6 8.2 - - - +
44P ALA* 1.3 83.1 - - - +
46P ALA* 1.3 70.1 + - - +
51P ARG* 3.3 9.9 + - - -
57P ALA* 4.4 7.1 + - - +
401P DDS 2.5 35.6 + - + +
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Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR* 3.6 2.6 - - - +
13P ALA* 4.1 5.8 - - - -
28P VAL 3.2 8.3 - - - +
29P VAL* 4.4 2.9 - - + -
43P VAL* 4.5 1.3 - - + +
45P THR* 1.3 78.0 + - - +
47P ASN* 1.3 61.7 + - - +
50P ALA* 3.5 19.5 - - + -
51P ARG* 2.9 32.1 + - + +
55P VAL* 3.5 35.4 - - + +
56P LYS* 4.8 0.7 - - - -
57P ALA 5.1 1.8 - - - +
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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