Contacts of the strand formed by residues 39 - 43 (chain D) in PDB entry 1II4
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 PHE 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TYR* 3.7 1.3 - - - -
34D CYS* 2.8 33.7 + - - +
36D ASN 3.3 16.2 - - - -
37D GLY* 3.6 17.5 - - - -
38D GLY* 1.3 79.9 - - - +
40D PHE* 1.3 59.4 + - - +
51D GLY 3.9 13.2 - - - -
52D VAL* 3.3 13.7 - - - +
53D ARG* 3.0 46.7 - - + -
127D LEU* 3.9 17.9 - - + +
128D LYS 4.3 2.2 - - - -
129D ARG 3.2 27.8 - - - -
130D THR 3.7 5.2 - - - -
131D GLY* 3.6 31.2 - - - -
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ARG* 3.7 36.8 - - + -
32D LEU 3.4 2.2 - - - +
33D TYR* 3.8 30.3 - + + -
38D GLY 4.9 1.8 - - - -
39D PHE* 1.3 73.2 - - - +
41D LEU* 1.3 63.6 + - - +
42D ARG 3.3 0.5 + - - -
51D GLY* 3.0 6.0 - - - -
52D VAL* 2.6 42.6 + - - +
53D ARG* 3.7 23.3 - - - -
55D LYS* 4.0 17.9 - - + -
60D ILE* 3.9 31.4 - - + -
127D LEU* 4.6 0.4 - - - -
151D MET* 3.9 14.1 - - + -
166H LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 41 (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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32D LEU* 2.8 46.9 + - + +
39D PHE 3.9 1.0 + - - -
40D PHE* 1.3 70.8 - - - +
42D ARG* 1.3 61.6 + - - +
43D ILE* 5.0 4.5 - - + -
49D VAL* 3.9 22.2 - - + -
50D ASP 3.6 15.7 - - - +
60D ILE* 3.5 22.4 - - - +
62D LEU* 4.1 15.4 - - + +
74D ILE* 4.8 3.1 - - + -
83D LEU* 4.4 24.0 - - + -
91D LEU* 5.6 0.7 - - + -
125D VAL* 4.4 15.9 - - + -
127D LEU* 4.3 20.1 - - + +
148D PHE* 4.2 8.7 - - + -
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Residues in contact with ARG 42 (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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40D PHE 3.3 3.1 + - - +
41D LEU* 1.3 74.7 - - - +
43D ILE* 1.3 66.7 + - - +
44D HIS* 2.9 30.6 + - + +
48D ARG* 3.9 0.5 - - - +
49D VAL* 3.5 7.1 - - - +
50D ASP* 2.6 76.3 + - - +
51D GLY* 4.4 0.6 + - - -
52D VAL* 2.9 27.8 - - + +
57D ASP* 2.9 34.4 + - - -
59D HIS* 3.4 23.1 - - + +
60D ILE* 3.8 8.7 - - + -
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Residues in contact with ILE 43 (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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41D LEU* 5.0 5.6 - - + -
42D ARG* 1.3 76.2 - - - +
44D HIS* 1.3 57.8 + - - +
48D ARG 3.8 2.2 - - - -
49D VAL* 4.5 8.1 - - + -
59D HIS* 2.8 27.9 + - - +
62D LEU* 3.9 15.9 - - + -
74D ILE* 4.0 17.3 - - + +
76D GLY* 3.5 34.3 - - - +
79D ALA* 3.0 29.6 + - + +
81D ARG 4.3 2.7 - - - +
83D LEU* 4.2 21.8 - - + +
93D ALA* 3.2 30.1 - - + -
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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