Contacts of the strand formed by residues 34 - 39 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.8 25.1 - - + -
22D CYS* 4.2 13.0 - - - +
24D ALA* 3.9 4.3 - - + -
27D TYR* 3.6 22.4 - - - +
29D PHE* 3.6 25.6 - - + -
32D TYR 3.7 1.9 + - - +
33D TYR* 1.3 73.2 - - - +
35D LYS* 1.3 62.7 + - - +
36D TRP* 4.2 12.4 - - + +
49D GLY 4.1 0.5 - - - +
50D ASP* 3.2 2.3 - - - -
51D ILE* 2.8 52.9 + - + +
52D PRO* 4.9 4.7 - - - +
78D ALA* 3.6 26.7 - - + -
92D CYS* 4.5 2.2 - - + -
93D ALA 3.4 21.1 - - - +
94D ASN* 4.5 1.8 - - - -
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Residues in contact with LYS 35 (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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28A ASP* 4.7 1.0 + - - -
91C SER* 5.9 1.0 + - - -
96C PHE* 4.1 18.2 - - - -
33D TYR* 4.3 13.5 - - - +
34D MET* 1.3 73.9 - - - +
36D TRP* 1.3 67.0 + - - +
37D VAL* 4.3 0.4 - - - -
47D TRP* 4.6 0.2 - - - +
49D GLY 3.6 4.0 - - - -
50D ASP* 2.8 40.0 + - + +
92D CYS* 3.1 7.1 - - - +
93D ALA* 2.7 36.9 + - - +
94D ASN* 4.5 13.5 - - - -
95D ASP* 4.5 12.3 - - - +
100D PHE* 3.9 55.5 + - - +
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Residues in contact with TRP 36 (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 GLN* 4.2 14.6 - - - -
20D MET* 4.4 14.4 - - + -
21D SER 4.5 1.3 - - - -
22D CYS* 3.6 21.3 - - + -
34D MET* 4.2 14.9 + - + +
35D LYS* 1.3 79.3 - - - +
37D VAL* 1.3 57.8 + - - +
47D TRP* 3.7 4.5 - - - -
48D ILE* 2.6 50.2 + - + +
49D GLY 2.9 13.1 + - - +
51D ILE* 4.9 2.8 - - - +
69D LEU* 3.4 35.0 - - + +
70D THR 5.6 0.2 + - - -
78D ALA* 3.8 28.3 - - + +
79D TYR 3.9 15.5 + - - -
80D MET* 3.8 37.2 - - + -
90D TYR 5.2 0.2 - - - -
91D TYR 3.3 18.4 - - - -
92D CYS* 3.7 15.0 - - + -
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Residues in contact with VAL 37 (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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98C PHE* 4.2 6.3 - - + -
36D TRP* 1.3 80.6 - - - +
38D LYS* 1.3 66.9 + - - +
45D LEU* 4.0 22.0 - - + -
46D GLU 3.0 29.2 - - - +
47D TRP* 4.7 2.0 - - - -
48D ILE* 4.0 3.4 - - - +
90D TYR* 3.3 4.5 - - - +
91D TYR* 2.7 39.1 + - + +
93D ALA* 5.2 3.1 - - + -
100D PHE* 3.7 33.2 - - - +
103D TRP* 3.9 25.1 - - + -
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Residues in contact with LYS 38 (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 VAL* 1.3 77.2 - - - +
39D GLN* 1.3 61.1 + - - +
40D SER* 3.8 19.7 - - - +
44D SER 3.8 0.7 - - - +
45D LEU* 3.5 1.9 - - - -
46D GLU* 2.8 56.7 + - + +
48D ILE* 3.7 11.2 - - + +
63D PHE* 4.2 19.8 - - + -
85D GLU* 3.4 25.5 + - - +
86D ASP* 4.6 5.3 + - - -
88D ALA* 4.1 12.3 - - + -
89D VAL 3.2 4.5 - - - -
90D TYR* 3.6 38.3 + - + +
91D TYR* 5.4 0.2 - - - -
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Residues in contact with GLN 39 (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* 2.8 44.7 + - - +
87C TYR* 3.6 12.5 + - - -
38D LYS* 1.3 74.3 - - - +
40D SER* 1.3 64.4 + - - +
41D HIS 4.2 0.9 + - - -
43D LYS* 3.7 22.0 - - - +
44D SER 3.5 16.8 - - - +
45D LEU* 3.7 21.6 - - + +
88D ALA* 3.1 2.7 - - - +
89D VAL* 2.7 39.5 + - + +
91D TYR* 3.4 24.5 + - + -
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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