Contacts of the strand formed by residues 76 - 80 (chain D) in PDB entry 1THF
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 PRO 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ASP 3.5 13.2 - - - +
46D GLU* 3.3 28.7 - - + +
47D LEU 3.0 21.7 + - - -
74D ASP 4.8 0.4 - - - +
75D ILE* 1.3 95.2 - - + +
77D PHE* 1.3 59.7 + - - +
98D ASP* 3.2 22.0 - - + +
99D LYS* 4.8 7.6 - - - -
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Residues in contact with PHE 77 (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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46D GLU* 5.3 0.2 - - - -
47D LEU* 3.2 14.8 - - + +
49D PHE* 3.7 33.4 - + + -
65D LEU* 5.1 0.7 - - + -
66D VAL* 4.1 14.1 - - + -
69D VAL* 3.7 20.2 - - + -
70D ALA* 3.9 18.2 - - - -
73D ILE* 3.6 20.2 - - + -
75D ILE 4.4 0.7 - - - -
76D PRO* 1.3 76.3 - - - +
78D THR* 1.3 61.5 + - - +
79D VAL* 4.1 15.9 - - + -
96D GLY 3.6 28.3 - - - -
97D ALA* 3.7 17.3 - - + -
98D ASP* 2.8 42.7 + - - +
99D LYS* 3.2 6.6 + - - +
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Residues in contact with THR 78 (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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46D GLU* 4.7 4.7 + - - -
47D LEU 2.9 10.7 + - - -
48D VAL* 3.4 19.1 - - + +
49D PHE* 2.8 27.9 + - - +
77D PHE* 1.3 74.1 - - - +
79D VAL* 1.3 68.0 + - - +
99D LYS* 3.2 38.7 - - + +
100D VAL 4.0 2.5 - - - -
101D SER* 3.8 30.5 - - - +
126D VAL* 4.3 9.4 - - + +
169D LEU* 5.6 1.8 - - + -
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Residues in contact with VAL 79 (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 PHE* 3.4 11.0 - - + +
62D MET* 3.9 22.4 - - + -
65D LEU* 4.9 0.4 - - + -
66D VAL* 3.7 24.0 - - + -
77D PHE* 4.1 14.8 - - + -
78D THR* 1.3 79.0 - - - +
80D GLY* 1.3 59.3 + - - +
83D ILE* 3.4 5.7 - - + +
92D LEU* 3.9 26.5 - - + -
97D ALA* 3.7 15.0 - - + -
99D LYS 3.0 12.4 + - - +
100D VAL* 3.9 4.9 - - + -
101D SER 2.9 22.5 + - - -
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Residues in contact with GLY 80 (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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48D VAL* 5.1 3.0 - - - +
49D PHE 2.9 10.4 + - - +
50D LEU* 3.8 11.0 - - - -
51D ASP* 2.9 24.6 + - - +
62D MET* 5.6 2.6 - - - +
78D THR* 4.2 0.6 - - - +
79D VAL* 1.3 75.6 - - - +
81D GLY* 1.3 63.4 + - - +
83D ILE* 4.1 5.8 - - - -
101D SER* 3.8 21.1 - - - -
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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