Contacts of the strand formed by residues 45 - 51 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B MET* 5.5 3.6 - - - -
29B PHE* 4.7 7.9 - - + -
30B PHE 3.4 8.3 - - - +
31B PHE* 4.3 19.3 - - + -
41B CYS* 3.4 6.1 - - - -
43B THR* 2.9 14.5 + - - +
44B GLY* 1.3 82.3 - - - +
46B PHE* 1.3 70.0 + - - +
60B ALA* 3.1 32.7 + - + -
62B PHE* 3.7 29.6 - - + -
69B LEU* 4.8 2.2 - - + -
110B MET* 4.5 12.6 - - + -
122B PHE* 4.4 17.7 - - + -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASN* 4.6 8.3 - - - -
14B LEU* 3.3 30.1 - - + -
29B PHE* 3.1 12.4 - - - -
30B PHE* 2.9 56.6 + + + +
33B GLN* 3.6 24.9 - - + -
40B SER* 5.6 2.5 - - - -
41B CYS* 3.5 30.1 - - + -
44B GLY 3.9 13.5 - - - -
45B VAL* 1.3 79.6 - - - +
47B HIS* 1.3 65.9 + - - +
57B LEU* 4.0 19.5 - - + -
58B LYS 3.4 7.0 - - - +
59B PRO* 3.8 21.8 - - + -
60B ALA* 4.2 0.9 - - - +
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLN* 3.3 37.4 + - + -
28B VAL 3.3 13.4 + - - -
29B PHE* 3.7 20.1 - + + -
46B PHE* 1.3 69.5 - - - +
48B PHE* 1.3 68.8 + - - +
49B ASP* 3.3 34.8 + - + +
56B LYS 3.2 6.6 - - - +
57B LEU* 3.3 3.5 - - - -
58B LYS* 2.8 49.3 + - + +
59B PRO 5.5 1.1 - - - +
60B ALA* 4.3 4.3 - - + +
118B LYS 5.9 2.5 - - - -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.8 2.5 - - + -
19B PHE* 5.0 0.4 - + - -
21B LEU* 3.9 19.1 - - + -
28B VAL* 2.9 48.6 + - + +
29B PHE 3.9 10.3 - - - -
30B PHE* 3.6 21.1 - + + +
46B PHE 3.4 0.2 + - - -
47B HIS* 1.3 72.9 + - - +
49B ASP* 1.3 58.9 + - - +
50B ILE* 4.1 5.9 + - + +
55B LEU* 3.7 24.9 - - + -
56B LYS 3.8 2.9 - - - -
57B LEU* 3.4 21.1 - - + -
322B MET* 3.9 23.7 - - + +
328B PHE* 3.7 40.2 - + - -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B HIS* 3.3 42.9 - - + +
48B PHE* 1.3 72.6 - - - +
50B ILE* 1.3 62.1 + - - +
51B LYS* 3.9 24.0 + - - +
54B HIS 3.5 2.4 - - - +
55B LEU* 3.9 0.6 - - - +
56B LYS* 2.9 59.2 + - - +
58B LYS* 4.4 14.7 + - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.2 12.1 - - + -
48B PHE* 4.1 12.7 + - + -
49B ASP* 1.3 74.3 - - - +
51B LYS* 1.3 68.7 + - - +
52B GLN 4.2 0.7 + - - -
53B ASN* 4.0 27.6 - - - +
54B HIS 3.3 7.9 - - - +
55B LEU* 3.8 17.5 - - + -
322B MET* 3.9 23.1 - - + +
328B PHE* 4.2 7.6 - - + -
347B THR* 3.6 29.2 - - + +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.9 26.4 + - - +
50B ILE* 1.3 77.5 + - - +
52B GLN* 1.3 75.7 + - + +
53B ASN 3.3 0.7 - - - -
54B HIS* 2.9 25.5 + - + +
56B LYS* 5.9 8.1 - - - +
40F C 5.5 0.9 + - - -
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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