Contacts of the strand formed by residues 63 - 69 (chain X) in PDB entry 4B3F
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 LEU 63 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55X GLN* 4.0 19.5 - - + +
56X ARG* 3.3 34.1 - - - +
57X THR* 3.3 18.2 - - + +
61X GLY 3.4 2.3 + - - +
62X ARG* 1.3 71.5 - - - +
64X LEU* 1.3 59.5 + - - +
65X VAL* 3.2 34.8 - - + -
116X VAL 3.5 0.5 - - - +
118X PHE* 3.1 48.6 + - + -
119X ASP* 5.2 2.8 - - + +
300X ILE* 4.2 5.6 - - + -
303X VAL* 6.2 0.9 - - + -
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Residues in contact with LEU 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X SER 3.7 1.4 - - - +
55X GLN* 3.3 2.6 - - - -
56X ARG* 2.9 42.6 + - + +
58X GLY* 4.1 22.4 - - - +
59X LEU* 4.8 4.7 - - + +
62X ARG* 4.5 7.6 - - + +
63X LEU* 1.3 70.1 - - - +
65X VAL* 1.3 63.5 + - - +
66X THR* 4.1 2.0 + - - +
107X THR* 4.2 19.3 - - + +
115X THR* 4.5 11.7 - - + -
116X VAL 3.4 3.4 - - - +
117X ALA* 3.5 31.2 - - + -
267X HIS* 6.1 4.0 - - + +
281X ASP* 6.1 1.1 - - - +
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Residues in contact with VAL 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL* 3.7 15.0 - - + -
54X SER 3.4 9.2 - - - +
55X GLN* 3.9 6.5 - - + +
63X LEU* 3.2 33.8 + - + -
64X LEU* 1.3 74.6 - - - +
66X THR* 1.3 65.2 + - - +
67X PHE* 3.7 16.8 - - + -
115X THR* 3.4 2.4 - - - -
116X VAL 2.9 31.5 + - - -
118X PHE* 3.5 24.9 - - + -
128X LEU* 3.7 28.7 - - + -
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Residues in contact with THR 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X VAL* 3.6 5.4 - - - +
53X SER* 2.8 39.1 + - - -
54X SER* 2.8 33.0 + - - +
64X LEU* 4.7 2.6 + - - +
65X VAL* 1.3 75.8 - - - +
67X PHE* 1.3 60.2 + - - +
113X SER* 4.3 20.0 - - - +
114X VAL 3.5 4.5 - - - +
115X THR* 3.6 26.9 + - - +
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Residues in contact with PHE 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X LEU* 4.1 36.3 - - + +
51X GLN 3.5 11.4 - - - -
52X VAL* 4.0 18.6 - - + -
65X VAL* 3.7 32.3 - - + -
66X THR* 1.3 79.8 - - - +
68X GLU* 1.3 59.9 + - - +
69X PRO* 4.9 0.2 - - - +
78X LEU* 5.2 1.9 - - - +
91X LEU* 3.9 19.3 - - + -
113X SER* 3.4 4.3 - - - -
114X VAL* 2.7 46.3 + - + +
116X VAL* 4.0 22.9 - - + -
118X PHE* 4.5 3.4 - + - -
128X LEU* 3.9 11.2 - - + -
134X TYR* 4.1 20.2 - + + -
136X LEU* 4.4 8.5 - - + -
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Residues in contact with GLU 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X LEU* 4.3 5.2 - - - -
51X GLN* 2.7 61.3 + - - +
53X SER* 3.4 30.5 + - - -
67X PHE* 1.3 75.4 - - - +
69X PRO* 1.3 79.3 - - + +
71X ARG* 5.5 1.2 + - - -
112X LYS 4.0 11.2 - - - +
113X SER* 4.9 2.9 - - - -
130X ARG* 5.9 1.4 + - - -
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Residues in contact with PRO 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LYS 4.2 9.2 - - - +
50X LEU* 4.5 3.1 - - + -
51X GLN* 4.1 0.7 - - - +
68X GLU* 1.3 99.7 - - + +
70X ARG* 1.3 73.9 + - - +
71X ARG* 3.5 1.0 + - - -
72X TYR* 4.4 12.1 - - + -
76X ALA* 4.0 21.9 - - + +
77X ALA 3.9 21.5 - - - +
78X LEU* 3.5 30.0 - - + -
79X PRO* 5.2 2.5 - - + -
112X LYS 3.9 10.3 - - - +
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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