Contacts of the strand formed by residues 92 - 98 (chain D) in PDB entry 3F12
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 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ARG* 4.2 13.7 - - + -
39D GLN 3.4 28.9 - - - +
40D ALA* 3.8 6.1 - - + +
41D PRO* 5.1 3.6 - - - -
89D GLU 5.2 0.9 - - - +
90D ASP 2.7 12.7 + - - +
91D THR* 1.3 76.9 + - - +
93D VAL* 1.3 62.5 + - - +
94D TYR* 3.3 10.5 - - + -
120D LEU* 3.9 8.3 - - - +
121D VAL 2.8 27.9 + - - +
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Residues in contact with VAL 93 (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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38D ARG* 3.3 4.2 - - - -
39D GLN* 2.9 41.6 + - + +
40D ALA 5.6 1.1 - - - +
41D PRO* 6.1 2.7 - - + -
92D ALA* 1.3 73.6 - - - +
94D TYR* 1.3 63.7 + - - +
95D TYR* 4.0 22.0 - - + +
117D GLN 4.9 1.1 - - - +
118D GLY* 4.5 8.1 - - - -
119D THR 3.6 23.1 - - - +
120D LEU* 3.1 26.2 - - + +
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Residues in contact with TYR 94 (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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6D GLU* 3.2 4.9 - - - +
20D LEU* 3.5 21.1 - - + -
36D TRP* 4.0 9.4 - + + -
37D VAL 3.9 3.4 - - - -
38D ARG* 2.6 52.1 + - + -
48D VAL* 4.3 9.2 - - + -
68D PHE* 4.1 3.1 - + - -
81D LEU* 3.9 20.0 - - + -
83D MET* 3.7 18.9 - - - -
90D ASP* 2.8 29.8 + - - +
92D ALA* 3.3 17.7 - - + -
93D VAL* 1.3 72.0 - - - +
95D TYR* 1.3 59.9 + - - +
118D GLY* 3.3 0.9 - - - -
119D THR* 2.8 39.7 + - + +
121D VAL* 3.4 24.0 - - + -
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Residues in contact with TYR 95 (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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38C GLN* 3.7 8.4 + - - -
42C GLN 5.5 0.7 - - - -
43C ALA* 4.2 5.6 - - + -
44C PRO* 4.0 15.3 - - + -
6D GLU* 2.7 9.4 - - - +
36D TRP* 3.4 9.6 - - - -
37D VAL 3.0 41.4 + - - +
38D ARG 4.7 0.2 - - - -
39D GLN* 2.4 47.7 + - + +
45D LEU* 4.3 9.6 - - + -
93D VAL* 4.0 19.4 - - + +
94D TYR* 1.3 71.8 - - - +
96D CYS* 1.3 61.4 + - - +
97D ALA* 5.4 0.2 - - - +
115D TRP* 3.9 29.2 - + + -
116D GLY 3.4 13.7 - - - +
117D GLN 2.9 29.8 - - - -
118D GLY* 3.9 3.6 - - - -
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Residues in contact with CYS 96 (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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4D LEU* 3.4 13.4 - - - +
5D VAL 4.3 0.9 - - - -
6D GLU* 2.7 29.0 + - - -
22D CYS* 2.0 54.7 - - + -
34D MET* 4.4 0.7 - - + -
35D HIS 3.3 10.8 - - - +
36D TRP* 4.2 11.7 - - + -
79D LEU* 4.2 4.9 - - + -
95D TYR* 1.3 74.7 - - - +
97D ALA* 1.3 60.4 + - - +
115D TRP* 3.8 1.2 - - - -
116D GLY 3.4 19.9 + - - -
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Residues in contact with ALA 97 (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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4D LEU* 3.9 0.2 - - - -
34D MET* 2.9 28.7 - - - +
35D HIS* 2.9 23.5 + - + -
37D VAL* 5.2 3.6 - - + -
95D TYR 4.0 0.8 + - - +
96D CYS* 1.3 75.6 - - - +
98D LYS* 1.3 61.4 + - - +
112D LEU* 3.1 31.9 - - + -
114D TYR 3.4 8.5 - - - +
115D TRP* 4.4 18.6 - - + -
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Residues in contact with LYS 98 (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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2D VAL* 4.9 2.7 - - + -
4D LEU* 4.2 6.3 - - + -
27D PHE* 3.7 41.1 - - + -
32D TYR* 3.9 17.7 - - + -
34D MET* 3.8 6.3 - - - -
35D HIS* 4.6 0.9 - - - -
97D ALA* 1.3 74.4 - - - +
99D ASP* 1.3 71.6 + - - +
112D LEU* 3.5 3.8 - - - -
113D ASP* 2.7 45.0 + - - +
114D TYR* 2.9 38.3 + - + +
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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