Contacts of the strand formed by residues 71 - 77 (chain T) in PDB entry 5HJD
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 TYR 71 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35T PHE* 3.2 3.0 - - - +
36T VAL* 2.8 46.4 + - + +
37T ARG* 5.3 0.4 - - - -
44T ILE* 3.8 30.3 - - + -
45T GLN* 3.5 33.6 - - - +
48T VAL* 3.8 18.9 + - + +
50T LYS* 4.6 1.3 - - - -
51T VAL* 3.6 35.4 - - + -
53T PHE* 3.4 7.6 - - + -
66T CYS* 3.8 26.5 - - + -
67T LYS* 4.1 4.6 + - - -
68T ASP 3.8 20.9 - - - -
69T PRO* 3.8 20.6 - - + +
70T PRO* 1.3 68.0 - - + +
72T LYS* 1.3 59.3 + - - +
202T SO4 5.3 0.4 + - - -
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Residues in contact with LYS 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T MET* 4.0 17.6 - - + -
34T VAL 3.2 14.1 - - - +
35T PHE* 3.6 12.8 - - + +
53T PHE* 4.0 4.3 - - - -
66T CYS* 3.6 15.0 - - - -
70T PRO* 3.1 34.9 + - + +
71T TYR* 1.3 74.9 - - - +
73T VAL* 1.3 64.0 + - - +
74T GLU* 3.9 29.6 + - + -
202T SO4 3.8 22.4 + - - +
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Residues in contact with VAL 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T TRP* 5.1 3.4 - - + -
33T MET* 3.3 20.4 - - - +
34T VAL* 3.1 26.1 + - + -
53T PHE* 3.5 35.2 - - + -
55T LEU* 4.4 8.5 - - + -
64T ARG* 3.5 50.9 - - + +
66T CYS* 4.8 3.1 - - - -
72T LYS* 1.3 77.7 - - - +
74T GLU* 1.3 66.2 + - - +
75T GLU* 4.1 12.6 - - + -
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Residues in contact with GLU 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T TRP 3.7 5.4 - - - +
33T MET* 3.7 25.0 - - + +
64T ARG* 4.7 0.9 + - - -
72T LYS* 3.9 26.4 + - + -
73T VAL* 1.3 82.3 - - - +
75T GLU* 1.3 74.8 + - - +
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Residues in contact with GLU 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H KCR 5.3 1.4 - - - +
31T ASP* 3.7 2.8 - - - +
32T TRP* 2.9 63.1 + - + +
55T LEU* 4.4 1.8 - - + -
59T PHE* 3.2 28.6 - - + -
60T PRO* 5.6 1.7 - - - +
64T ARG* 3.2 39.3 + - - +
73T VAL* 4.1 7.6 - - + -
74T GLU* 1.3 83.1 - - - +
76T SER* 1.3 68.1 + - - +
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Residues in contact with SER 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H KCR 4.1 1.9 - - - +
20T ARG* 3.7 11.2 + - - -
24T THR* 4.8 3.3 - - - +
28T PHE* 3.8 29.7 - - - -
30T HIS 3.3 7.0 - - - -
31T ASP* 2.9 23.5 + - - -
32T TRP* 4.0 3.6 - - - +
59T PHE* 3.8 15.1 - - - -
75T GLU* 1.3 79.2 + - - +
77T GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H KCR 3.3 14.4 - - - -
28T PHE* 3.9 11.4 - - - +
29T THR 3.0 6.1 + - - -
30T HIS* 2.9 34.3 + - - +
32T TRP* 3.6 15.7 - - - +
59T PHE* 4.7 0.9 - - - -
76T SER* 1.3 73.7 - - - +
78T TYR* 1.3 60.5 + - - -
79T ALA 3.8 1.8 - - - -
106T LEU* 5.1 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