Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 6CIM
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D MET* 5.4 2.5 - - - -
29D PHE* 4.5 10.5 - - + -
30D PHE 3.5 8.3 - - - +
31D PHE* 4.2 21.3 - - + -
41D CYS* 3.6 3.0 - - - -
43D THR* 3.0 12.1 + - - +
44D GLY* 1.3 82.7 - - - +
46D PHE* 1.3 68.5 + - - +
60D ALA* 3.1 24.3 + - + +
62D PHE* 3.5 32.1 - - + -
69D LEU* 4.8 2.0 - - + -
110D MET* 4.5 10.8 - - + -
122D PHE* 4.1 28.3 - - + -
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 4.6 7.9 - - - -
14D LEU* 3.5 28.3 - - + -
29D PHE* 3.1 13.1 - - - -
30D PHE* 2.9 57.4 + + + +
33D GLN* 3.4 25.4 - - + -
40D SER* 5.9 1.1 - - - -
41D CYS* 3.5 32.5 - - + -
44D GLY 3.9 13.5 - - - -
45D VAL* 1.3 76.1 - - - +
47D HIS* 1.3 61.4 + - - +
48D PHE 3.4 0.2 + - - -
57D LEU* 4.2 23.8 - - + -
58D LYS 3.4 20.9 - - - +
59D PRO* 3.9 9.2 - - + -
60D ALA* 4.4 0.9 - - - +
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLN* 2.9 44.2 + - + -
28D VAL 3.8 8.2 + - - -
29D PHE* 3.7 26.2 - - + -
46D PHE* 1.3 70.1 - - - +
48D PHE* 1.3 58.1 + - - +
49D ASP* 2.6 43.3 + - + -
56D LYS 3.2 8.1 - - - +
57D LEU* 3.4 2.3 - - - -
58D LYS* 2.8 56.2 + - + +
59D PRO 5.5 1.1 - - - +
60D ALA* 4.6 2.9 - - + +
118D LYS 4.8 8.9 + - - +
119D LYS* 6.6 0.4 - - - -
120D VAL* 5.9 0.2 - - - +
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ILE* 5.2 2.2 - - + -
19D PHE* 5.3 0.7 - + - -
21D LEU* 3.8 22.0 - - + -
28D VAL* 2.9 49.1 + - + +
29D PHE 4.2 0.2 - - - -
30D PHE* 3.9 20.2 - + + -
46D PHE 3.4 0.6 + - - -
47D HIS* 1.3 69.8 + - - +
49D ASP* 1.3 59.7 + - - +
50D ILE* 3.6 11.8 + - + -
55D LEU* 3.6 22.4 - - + -
56D LYS 3.9 2.5 - - - -
57D LEU* 3.6 18.4 - - + -
322D MET* 3.4 30.4 - - + +
328D PHE* 3.6 39.7 - + - -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D HIS* 2.6 36.7 + - + -
48D PHE* 1.3 72.1 - - - +
50D ILE* 1.3 64.6 + - - +
51D LYS* 3.3 36.5 + - + +
54D HIS 3.4 2.6 - - - +
55D LEU* 3.5 1.2 - - - +
56D LYS* 2.9 46.3 + - + +
58D LYS* 5.0 12.0 + - - -
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D VAL* 4.1 11.0 - - + -
48D PHE* 3.6 31.6 + - + -
49D ASP* 1.3 75.6 + - - +
51D LYS* 1.3 71.3 + - - +
52D GLN 4.3 0.7 + - - -
53D ASN* 3.9 27.6 - - - +
54D HIS 3.3 7.2 - - - +
55D LEU* 3.9 10.3 - - + -
322D MET* 3.8 13.5 - - + -
328D PHE* 4.1 9.2 - - + -
347D THR* 3.7 29.4 - - + +
349D ARG* 6.1 1.8 - - - +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ASP* 3.3 32.2 + - + +
50D ILE* 1.3 80.4 + - - +
52D GLN* 1.3 80.3 + - + +
53D ASN 3.3 0.9 - - - -
54D HIS* 2.9 25.6 + - - +
56D LYS* 5.9 6.3 - - - -
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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