Contacts of the strand formed by residues 49 - 56 (chain D) in PDB entry 2CFX
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 ILE 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ILE* 5.0 0.2 - - + -
11D ILE* 4.5 12.3 - - + -
14D LEU* 4.1 19.3 - - + -
40D VAL* 4.6 5.4 - - + -
43D LEU* 3.4 31.8 + - + -
44D GLU* 3.8 28.2 - - + +
47D GLY* 3.9 4.2 - - - -
48D ILE* 1.3 79.1 + - - +
50D LYS* 1.3 61.8 + - - +
51D GLN 4.1 6.1 - - - +
52D TYR* 3.8 40.6 - - + +
54G LEU* 3.8 29.6 - - + -
55G GLU 3.7 3.1 - - - -
56G VAL* 4.7 1.1 - - + +
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Residues in contact with LYS 50 (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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47D GLY* 3.6 21.5 - - - +
48D ILE 3.6 0.2 + - - -
49D ILE* 1.3 75.2 - - - +
51D GLN* 1.3 59.1 - - - +
55G GLU* 2.7 48.8 + - - +
56G VAL 3.5 22.6 + - - -
57G ASP* 4.0 21.4 + - - +
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Residues in contact with GLN 51 (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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49D ILE* 3.6 2.1 - - - +
50D LYS* 1.3 80.1 - - - +
52D TYR* 1.3 79.1 + - - +
53D THR* 3.8 9.1 + - - -
15G LYS* 3.1 23.4 + - - +
16G LYS* 3.5 20.9 + - - +
54G LEU* 3.4 6.9 - - - +
55G GLU* 2.9 52.5 + - + +
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Residues in contact with TYR 52 (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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14D LEU* 3.9 14.5 - - + +
18D SER* 3.7 13.9 - - - -
22D MET* 6.0 0.2 - - - +
40D VAL* 3.4 22.5 - - - +
44D GLU* 3.1 29.7 + - + -
49D ILE* 3.8 22.5 - - + +
51D GLN* 1.3 74.7 - - - +
53D THR* 1.3 61.0 + - - +
15G LYS 3.4 6.1 - - - +
16G LYS 3.5 3.3 + - - +
17G ASP* 3.4 25.0 - - - +
18G SER* 3.2 22.4 + - - +
19G ARG* 3.4 49.6 + - + -
53G THR 3.6 3.1 - - - +
54G LEU* 3.7 19.7 - - + -
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Residues in contact with THR 53 (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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51D GLN* 3.8 17.4 + - - -
52D TYR* 1.3 76.3 - - - +
54D LEU* 1.3 68.9 + - - +
15G LYS* 3.0 20.1 + - - +
18G SER* 2.7 17.1 + - - -
52G TYR* 3.5 0.5 - - - -
53G THR* 2.7 58.1 + - + -
54G LEU 3.7 15.9 - - - +
55G GLU* 4.1 6.3 - - + +
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Residues in contact with LEU 54 (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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53D THR* 1.3 84.5 + - - +
55D GLU* 1.3 62.1 + - - +
56D VAL* 3.8 26.9 + - + +
11G ILE* 4.2 11.0 - - + +
14G LEU* 3.6 29.6 - - + -
15G LYS* 3.9 27.7 - - + +
18G SER* 3.7 6.1 - - - -
49G ILE* 4.0 20.0 - - + -
51G GLN 3.5 5.6 - - - +
52G TYR* 3.5 38.1 - - + -
53G THR* 4.3 3.6 - - - -
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Residues in contact with GLU 55 (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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54D LEU* 1.3 73.8 - - - +
56D VAL* 1.3 58.4 + - - +
49G ILE* 3.6 3.6 - - - +
50G LYS* 2.6 68.5 + - + +
51G GLN* 2.7 47.5 + - + +
53G THR* 4.3 13.3 + - + +
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Residues in contact with VAL 56 (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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54D LEU* 3.8 31.0 - - + +
55D GLU* 1.3 76.9 - - - +
57D ASP* 1.3 64.6 + - - +
58D GLN* 3.5 23.0 + - - +
61D LEU* 3.0 33.2 - - + -
11G ILE* 3.9 17.5 - - + -
15G LYS* 4.5 13.0 - - - +
48G ILE* 3.0 15.3 - - + +
49G ILE* 4.6 1.8 - - + -
50G LYS* 3.6 15.4 + - - -
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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