Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 1F11
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 MET 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.9 24.7 - - + -
22B CYS* 4.1 11.0 - - - +
24B ALA* 3.9 4.0 - - + -
27B TYR* 3.6 17.5 - - - +
29B PHE* 3.6 30.7 - - + -
32B TYR 3.7 1.0 + - - +
33B TYR* 1.3 73.2 - - - +
35B LYS* 1.3 62.3 + - - +
36B TRP* 4.2 12.6 - - + +
49B GLY 4.1 0.2 - - - +
50B ASP* 3.2 1.7 - - - -
51B ILE* 2.8 53.1 + - + +
52B PRO* 4.9 5.2 - - - +
78B ALA* 3.7 26.7 - - + -
92B CYS* 4.6 1.6 - - + -
93B ALA 3.5 15.5 - - - +
94B ASN* 4.4 1.8 - - - -
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.2 19.0 - - - -
33B TYR* 4.4 13.9 - - - +
34B MET* 1.3 75.9 - - - +
36B TRP* 1.3 64.1 + - - +
37B VAL* 4.4 0.7 - - - -
47B TRP* 4.6 0.2 - - - +
49B GLY 3.6 3.6 - - - -
50B ASP* 2.9 38.9 + - + +
92B CYS* 3.1 6.8 - - - +
93B ALA* 2.7 40.2 + - - +
94B ASN* 4.5 14.1 - - - -
95B ASP* 4.5 11.9 - - - -
100B PHE* 3.9 55.1 + - - +
28C ASP* 4.3 2.6 + - - -
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Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 4.2 14.1 - - - -
20B MET* 4.4 12.3 - - + -
21B SER 4.5 1.8 - - - -
22B CYS* 3.6 23.1 - - + -
34B MET* 4.2 16.1 + - + +
35B LYS* 1.3 77.5 - - - +
37B VAL* 1.3 58.2 + - - +
47B TRP* 3.6 5.4 - - - -
48B ILE* 2.7 49.9 + - + +
49B GLY 2.9 11.6 + - - +
51B ILE* 5.0 3.4 - - - +
69B LEU* 3.6 34.8 - - + +
70B THR 5.6 0.2 + - - -
78B ALA* 3.8 28.5 - - + +
79B TYR 3.9 15.1 + - - -
80B MET* 3.7 39.3 - - + -
91B TYR 3.3 17.9 - - - -
92B CYS* 3.7 15.3 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.3 5.6 - - + -
35B LYS 5.3 0.9 - - - -
36B TRP* 1.3 80.5 - - - +
38B LYS* 1.3 63.1 + - - +
45B LEU* 3.9 22.7 - - + -
46B GLU 3.0 33.4 - - - +
47B TRP* 4.7 2.5 - - - -
48B ILE* 4.0 4.2 - - - +
90B TYR* 3.3 4.9 - - - +
91B TYR* 2.8 37.2 + - + +
93B ALA* 5.3 2.2 - - + -
100B PHE* 3.7 32.5 - - - +
103B TRP* 4.0 24.0 - - + -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 1.3 76.2 - - - +
39B GLN* 1.3 59.4 + - - +
40B SER* 3.9 19.5 - - - +
44B SER 3.8 1.0 - - - +
45B LEU* 3.6 1.6 - - - -
46B GLU* 2.8 57.0 + - + +
48B ILE* 3.8 10.5 - - + +
63B PHE* 4.1 20.5 - - + -
85B GLU* 3.4 24.3 + - - +
86B ASP* 4.6 8.9 + - - +
88B ALA* 4.1 11.4 - - + -
89B VAL 3.2 5.4 - - - -
90B TYR* 3.5 36.1 - - + +
91B TYR* 5.4 0.2 - - - -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.0 42.3 + - - -
87A TYR* 3.8 4.6 + - - -
38B LYS* 1.3 74.5 - - - +
40B SER* 1.3 65.5 + - - +
41B HIS 4.2 0.7 + - - -
43B LYS* 3.7 30.5 - - - +
44B SER 3.5 19.1 - - - +
45B LEU* 3.7 22.0 - - + +
88B ALA* 3.1 2.3 - - - +
89B VAL* 2.7 43.3 + - + +
91B TYR* 3.4 22.6 + - + -
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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