Contacts of the strand formed by residues 48 - 55 (chain B) in PDB entry 4GE7
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 PHE 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.8 17.7 - - + -
54A THR 3.6 4.3 - - - -
55A VAL* 4.2 4.9 - - + -
61A ILE* 3.6 27.4 - - + -
265A ILE* 3.8 24.7 - - + -
269A LEU* 3.9 14.4 - - + -
302A MET* 3.7 31.4 - - + -
303A ILE* 4.2 5.8 - - + -
306A LEU* 3.7 24.5 - - + -
46B PHE* 3.5 3.2 - - - +
47B PRO* 1.4 80.6 - - + +
49B LYS* 1.4 63.8 + - - +
68B MET* 3.6 23.1 - - + +
72B LEU* 3.3 39.0 - - + +
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Residues in contact with LYS 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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54A THR* 2.9 21.3 + - - +
55A VAL 4.8 0.7 - - - -
56A GLU* 3.4 48.7 + - + +
43B PRO 4.8 1.2 + - - -
44B ASN* 3.1 27.7 + - - +
46B PHE 2.9 25.5 + - - -
47B PRO* 3.9 6.7 - - - +
48B PHE* 1.4 75.3 - - - +
50B THR* 1.3 69.1 + - + +
65B GLU* 3.8 13.3 - - + +
68B MET* 3.2 22.1 - - - +
69B LYS* 6.2 3.0 - - - +
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Residues in contact with THR 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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52A VAL 4.6 0.2 - - - -
53A ILE* 3.3 4.0 - - - -
54A THR* 2.6 54.0 + - - +
49B LYS* 1.3 83.3 - - + +
51B ALA* 1.3 61.8 + - - +
52B VAL* 5.6 4.0 - - - +
63B PHE 3.3 15.9 - - - +
64B GLY* 4.2 2.7 - - - -
65B GLU* 4.1 23.6 - - + +
68B MET* 3.4 10.7 - - - +
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Residues in contact with ALA 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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52A VAL 3.4 7.2 - - - -
53A ILE* 4.0 13.9 - - + -
50B THR* 1.3 75.5 - - - +
52B VAL* 1.3 64.0 + - - +
53B ILE* 4.3 9.6 - - + +
61B ILE 4.5 0.2 - - - -
62B GLN* 3.5 3.3 - - - +
63B PHE* 2.7 50.1 + - + +
68B MET* 3.8 15.5 - - + -
298B PHE* 4.1 13.5 - - + -
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Residues in contact with VAL 52 (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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50A THR 4.1 0.2 - - - +
51A ALA* 3.4 2.9 - - - -
52A VAL* 3.0 52.2 + - + +
50B THR* 5.6 4.3 - - - +
51B ALA* 1.3 76.6 - - - +
53B ILE* 1.3 62.7 + - - +
54B THR* 4.3 8.5 + - + +
60B THR* 3.9 15.0 - - - +
61B ILE 3.4 2.5 - - - -
62B GLN* 3.9 28.5 - - + +
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Residues in contact with ILE 53 (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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48A PHE* 3.8 22.9 - - + -
50A THR 3.4 12.8 - - - +
51A ALA* 4.0 15.9 - - + -
53A ILE* 6.2 0.7 - - + -
68A MET* 3.7 16.6 - - + -
298A PHE* 4.8 2.0 - - + -
51B ALA* 4.6 11.0 - - + -
52B VAL* 1.3 77.2 - - - +
54B THR* 1.3 67.4 + - - +
55B VAL* 4.0 1.5 - - + +
60B THR* 3.4 3.3 + - - -
61B ILE* 2.8 55.9 + - + +
63B PHE* 5.0 3.4 - - + -
298B PHE* 4.4 15.7 - - + -
302B MET* 3.8 32.8 - - + -
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Residues in contact with THR 54 (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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48A PHE* 3.6 4.9 - - - -
49A LYS* 2.9 33.4 + - - +
50A THR* 2.6 40.7 + - - +
52B VAL* 5.0 9.4 - - + +
53B ILE* 1.3 75.3 - - - +
55B VAL* 1.3 61.3 + - - +
60B THR* 4.2 14.8 - - - +
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Residues in contact with VAL 55 (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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47A PRO* 3.3 11.9 - - + +
48A PHE* 4.2 11.9 - - + -
49A LYS* 4.7 2.5 - - - -
53B ILE 3.8 3.6 + - - +
54B THR* 1.3 79.6 - - - +
56B GLU* 1.4 70.8 + - - +
57B ASN 3.7 1.4 + - - +
58B GLY* 3.3 29.1 - - - +
59B LYS 3.8 18.4 - - - +
60B THR* 4.6 4.2 - - - +
61B ILE* 3.7 31.9 - - + -
306B LEU* 3.7 22.4 - - + -
310B TRP* 4.9 1.3 - - - +
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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