Contacts of the strand formed by residues 27 - 34 (chain D) in PDB entry 3FTN
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 ALA 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D PRO* 4.5 0.9 - - - -
26D ASP* 1.3 75.6 - - - +
28D ILE* 1.3 67.8 + - - +
29D VAL* 4.4 5.2 - - + -
65D VAL* 4.4 6.7 - - + -
67D GLU 3.1 12.3 - - - +
68D VAL* 3.9 12.3 - - + -
75D PHE* 5.8 0.2 - - + -
125D HIS* 3.8 0.2 - - - -
126D VAL* 2.9 34.6 + - + +
129D ALA* 3.7 21.2 - - + +
133D LEU* 4.1 14.4 - - + -
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Residues in contact with ILE 28 (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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19D LYS* 4.6 5.2 - - - -
20D PRO* 3.2 35.4 - - + +
21D ALA 3.9 10.3 - - - -
22D PRO* 3.4 21.8 - - + -
27D ALA* 1.3 79.9 - - - +
29D VAL* 1.3 59.4 + - - +
65D VAL* 3.7 1.0 - - - +
66D VAL* 2.7 44.9 + - + -
67D GLU* 2.7 27.7 + - + +
123D PHE* 4.0 22.7 - - + -
124D PHE 3.5 10.8 - - - +
125D HIS* 4.1 14.8 - - + -
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Residues in contact with VAL 29 (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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27D ALA* 4.2 12.6 - - + +
28D ILE* 1.3 80.3 - - - +
30D ARG* 1.3 63.5 - - - +
63D GLY* 3.9 6.5 - - - -
64D GLU 3.6 26.9 - - - +
65D VAL* 4.6 5.6 - - - -
66D VAL* 4.9 0.2 - - - -
81D VAL* 4.2 9.2 - - + -
83D VAL* 4.7 0.7 - - + -
123D PHE* 3.4 6.1 - - - -
124D PHE* 2.9 60.5 + - + -
126D VAL* 3.7 26.5 - - + -
133D LEU* 4.6 10.3 - - + -
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Residues in contact with ARG 30 (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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19D LYS* 5.7 0.2 - - - +
29D VAL* 1.3 74.4 - - - +
31D PRO* 1.3 69.8 - - - +
32D LEU* 4.7 3.8 - - + -
63D GLY* 3.1 2.0 - - - -
64D GLU* 2.7 74.1 + - + +
66D VAL* 3.8 17.7 - - + +
122D GLU* 3.6 17.6 + - - +
123D PHE* 3.3 44.6 - - + -
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Residues in contact with PRO 31 (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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29D VAL 4.1 2.9 - - - +
30D ARG* 1.3 90.6 - - + +
32D LEU* 1.3 65.2 + - - +
34D VAL* 3.7 27.1 - - + -
61D ALA* 4.6 0.2 - - + -
62D VAL 3.6 7.6 - - - +
63D GLY* 3.8 1.8 - - - -
119D VAL 3.6 11.9 - - - +
121D GLY 3.3 19.1 - - - +
122D GLU* 3.3 18.8 - - - +
124D PHE* 3.9 15.2 - - + -
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Residues in contact with LEU 32 (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 ARG* 4.7 4.3 - - + -
31D PRO* 1.3 80.1 - - - +
33D ALA* 1.3 63.2 + - - +
62D VAL* 2.8 12.0 + - + +
63D GLY* 4.0 25.6 - - - +
64D GLU* 3.9 28.9 - - + +
80D ARG* 3.6 45.1 - - + +
142D LEU* 4.1 21.2 - - + +
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Residues in contact with ALA 33 (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 PRO 3.6 0.2 - - - -
32D LEU* 1.3 81.8 - - - +
34D VAL* 1.3 69.6 + - - +
61D ALA* 3.3 0.3 - - - -
62D VAL* 3.0 47.2 + - + +
142D LEU* 4.0 23.8 - - + +
143D GLU* 5.4 0.9 - - - +
146D VAL* 3.7 9.1 - - + +
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Residues in contact with VAL 34 (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 PRO* 3.7 25.4 - - + -
33D ALA* 1.3 83.3 - - - +
35D ALA* 1.3 62.3 + - - +
60D GLU 3.2 13.7 - - - +
61D ALA* 4.0 6.5 - - + -
119D VAL* 4.2 13.0 - - + +
120D PHE* 3.6 26.2 - - + -
146D VAL* 3.9 8.4 - - - +
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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