Contacts of the strand formed by residues 74 - 80 (chain D) in PDB entry 3TDD
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 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D GLU* 3.8 0.9 - - - +
70D ILE* 2.8 45.8 + - + -
71D ASP* 2.8 18.5 + - + +
72D ARG 3.5 0.6 + - - -
73D HIS* 1.3 112.7 - - + +
75D GLY* 1.3 63.3 + - - +
107D ILE* 4.2 6.1 - - + -
109D VAL* 4.1 22.4 - - + -
112D LEU* 3.8 31.0 - - + -
138D ILE* 3.7 24.0 - - + -
139D ALA 3.4 9.9 - - - +
140D GLY* 4.4 0.4 - - - -
221D PHE* 4.5 3.8 - - - +
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Residues in contact with GLY 75 (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 LEU* 4.1 6.1 - - - -
68D VAL 3.4 7.9 - - - -
70D ILE* 4.2 1.8 - - - -
74D ILE* 1.3 78.0 - - - +
76D CYS* 1.3 63.9 + - - +
138D ILE* 3.8 1.0 - - - -
139D ALA 2.8 31.5 + - - +
215D ILE* 5.1 0.4 - - - +
221D PHE* 3.3 28.1 - - - +
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Residues in contact with CYS 76 (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 LEU* 3.8 7.4 - - - +
66D LYS 4.0 0.3 - - - +
67D ILE* 3.3 4.7 - - - +
68D VAL* 2.8 39.1 + - - +
70D ILE* 3.9 18.2 - - + -
75D GLY* 1.3 77.1 - - - +
77D ALA* 1.3 64.0 + - - +
78D MET* 4.9 1.5 - - - +
89D ILE* 3.8 23.3 - - - -
136D LEU* 3.8 33.9 - - - -
137D LEU 3.2 11.0 - - - +
138D ILE* 4.0 7.6 - - + -
221D PHE* 4.3 1.0 - - - -
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Residues in contact with ALA 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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37D ALA* 4.4 8.7 - - + -
38D ILE 5.7 0.2 - - - +
48D LEU* 3.8 21.5 - - + +
49D GLY 5.1 0.9 - - - +
50D VAL* 3.8 24.5 - - + -
66D LYS 3.4 4.7 - - - +
67D ILE* 4.5 2.7 - - + -
76D CYS* 1.3 78.3 - - - +
78D MET* 1.3 61.5 + - - +
136D LEU* 3.3 5.7 - - - +
137D LEU* 2.8 41.5 + - + +
165D ILE* 4.6 0.3 - - - +
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Residues in contact with MET 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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35D SER* 4.8 1.6 - - - +
36D THR 5.5 0.2 - - - +
37D ALA* 3.9 10.6 - - - +
50D VAL* 4.7 1.6 - - - +
65D GLU 3.9 10.5 - - - +
66D LYS* 3.1 44.1 + - + +
68D VAL* 4.1 19.7 - - + +
76D CYS* 5.2 0.9 - - - +
77D ALA* 1.3 75.1 - - - +
79D SER* 1.3 64.0 + - - +
82D THR* 3.9 24.4 - - + +
85D ALA* 4.0 17.3 - - + -
86D ARG* 3.9 29.8 - - - +
89D ILE* 4.6 5.8 - - + -
134D VAL* 3.9 7.0 - - + -
135D ALA 3.4 5.2 - - - -
136D LEU* 3.5 15.9 - - + -
165D ILE* 4.6 0.4 - - - -
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Residues in contact with SER 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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31D ILE* 3.6 9.2 + - - +
34D GLY* 3.8 2.9 - - - -
35D SER* 2.6 29.1 + - - +
37D ALA* 4.2 1.3 - - - -
66D LYS* 6.3 0.2 - - - -
78D MET* 1.3 79.9 - - - +
80D GLY* 1.3 60.0 + - - +
82D THR* 5.4 1.8 - - - -
134D VAL* 3.2 3.8 - - - +
135D ALA 3.0 29.8 + - - -
165D ILE* 3.5 28.0 - - - -
166D GLY* 3.3 16.7 - - - -
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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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30D ALA 4.4 3.4 - - - -
31D ILE* 4.1 12.3 - - - -
34D GLY* 3.8 22.2 - - - -
35D SER 4.7 0.8 + - - +
79D SER* 1.3 77.2 + - - +
81D LEU* 1.3 62.9 + - - -
82D THR* 3.0 16.6 + - - +
133D GLY 3.6 5.6 - - - -
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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