Contacts of the strand formed by residues 34 - 41 (chain D) in PDB entry 5E94
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 ASP 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D TYR* 1.3 76.1 - - - +
35D TRP* 1.3 66.6 + - - +
36D HIS* 3.8 7.0 - - - +
51D TYR* 4.2 11.3 - - + -
52D ILE 3.8 3.6 - - - -
53D SER* 3.2 20.7 - - - -
54D TYR 4.1 0.2 + - - -
98D ARG* 3.8 2.9 - - - +
99D ALA* 2.9 32.0 + - - +
108D TYR* 2.6 29.1 + - - +
31H SER* 4.1 2.9 - - - -
32H LEU* 2.9 25.4 + - - +
33H TRP* 2.9 26.7 + - - +
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Residues in contact with TRP 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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2D VAL* 4.7 3.1 - - + -
4D LEU* 4.2 8.1 - - + -
24D VAL* 3.7 31.0 - - + -
27D TYR* 5.0 4.7 - + + -
28D SER 4.2 5.6 - - - -
29D ILE* 3.3 46.6 + - + -
31D SER 5.0 0.2 - - - -
33D TYR* 3.6 33.6 + + + +
34D ASP* 1.3 76.2 - - - +
36D HIS* 1.3 61.2 + - - +
51D TYR* 3.2 1.9 - - - -
52D ILE* 2.8 51.5 + - + +
53D SER 4.4 3.4 - - - -
70D ILE* 5.0 1.2 - - - +
79D PHE* 3.6 45.5 - + + -
97D ALA 3.6 3.4 - - - -
98D ARG* 3.5 41.5 - - + -
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Residues in contact with HIS 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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96C PHE* 3.8 10.1 - + - -
34D ASP* 3.8 5.1 - - - +
35D TRP* 1.3 78.8 - - - +
37D TRP* 1.3 63.3 + - - +
38D ILE* 4.3 11.2 - - + -
48D TRP* 2.7 30.6 + - - +
50D GLY 3.3 4.3 - - - +
51D TYR* 3.4 29.5 - + + +
79D PHE* 3.7 2.1 - - - -
96D CYS* 3.2 8.8 - - - +
97D ALA* 2.9 34.8 + - - +
99D ALA* 3.5 22.6 - - + +
108D TYR* 2.8 24.8 + - - -
110D PHE* 3.4 24.3 - + + -
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Residues in contact with TRP 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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6D GLU* 4.0 12.6 - - + -
20D LEU* 3.9 28.9 - - + -
21D THR 3.9 3.6 - - - -
22D CYS* 3.8 26.2 - - + -
36D HIS* 1.3 75.9 - - - +
38D ILE* 1.3 65.9 + - - +
48D TRP* 4.1 0.9 - - - -
49D MET* 2.9 38.4 + - + +
50D GLY 3.0 11.1 + - - +
70D ILE* 3.8 24.5 - - + -
79D PHE* 3.5 35.9 - + - -
80D PHE 3.5 12.5 + - - -
81D LEU* 3.4 45.8 - - + -
94D TYR* 4.8 3.8 - - + -
95D TYR 3.3 26.2 - - - -
96D CYS* 3.8 12.6 - - + -
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Residues in contact with ILE 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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98C PHE* 4.1 19.5 - - + -
36D HIS* 4.3 4.7 - - + -
37D TRP* 1.3 80.3 - - - +
39D ARG* 1.3 69.2 + - - +
40D HIS* 6.2 0.2 - - + -
46D LEU* 4.9 7.6 - - + -
47D GLU 3.5 12.6 - - - +
48D TRP* 4.1 16.4 - - + -
49D MET* 4.4 2.5 - - - -
94D TYR* 3.6 1.0 - - - +
95D TYR* 2.6 44.2 + - + +
97D ALA* 4.0 18.4 - - + -
110D PHE* 4.2 21.5 - - + -
113D TRP* 3.5 41.1 - - + -
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Residues in contact with ARG 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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38D ILE* 1.3 76.9 - - - +
40D HIS* 1.3 61.8 + - - +
41D PHE* 3.1 32.3 - - + -
45D ILE 4.0 0.9 - - - +
46D LEU* 3.4 4.2 - - - +
47D GLU* 2.7 69.9 + - + +
49D MET* 3.7 13.1 - - + +
64D LEU* 3.7 21.1 - - - +
67D ARG* 4.3 2.2 - - - +
83D LEU* 3.6 11.1 - - - +
89D GLU 5.2 0.4 + - - -
90D ASP* 3.0 28.7 + - - +
92D ALA* 4.2 2.2 - - + -
93D THR 3.2 9.0 - - - +
94D TYR* 3.0 49.1 + - + -
95D TYR* 5.4 0.2 - - - -
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Residues in contact with HIS 40 (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 27.1 + - - +
87C PHE* 4.3 1.2 - + - -
39D ARG* 1.3 74.7 - - - +
41D PHE* 1.3 75.6 + - - +
42D PRO* 4.6 1.1 - - + +
44D ASN* 2.9 38.2 + - - -
45D ILE 3.6 2.0 - - - -
46D LEU* 3.1 34.5 - - + +
92D ALA* 3.4 3.0 - - - +
93D THR* 2.8 48.6 + - - +
95D TYR* 4.3 16.6 + - + -
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Residues in contact with PHE 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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39D ARG* 3.1 44.2 - - + -
40D HIS* 1.3 86.1 + - - +
42D PRO* 1.3 78.9 - - + +
44D ASN 3.3 12.6 + - - -
45D ILE* 2.8 46.9 + - + +
47D GLU* 3.9 23.1 - - + -
89D GLU 3.4 22.9 - - - -
90D ASP* 4.7 0.4 - - - -
91D THR 3.4 16.6 - - - -
92D ALA* 3.6 13.2 - - + -
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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