Contacts of the strand formed by residues 44 - 52 (chain D) in PDB entry 3DIF
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 GLY 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C TYR* 4.4 18.2 - - - -
99C GLY 5.4 2.0 - - - -
100C GLY* 5.2 7.2 - - - -
38D LYS 3.5 1.4 - - - +
39D GLN* 2.7 29.5 + - - -
40D ARG 3.2 19.3 + - - -
41D PRO 4.8 1.6 + - - -
42D GLY 3.7 1.0 - - - -
43D GLN* 1.3 79.1 - - - +
45D LEU* 1.3 57.4 + - - -
46D GLU* 5.1 1.4 - - - +
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Residues in contact with LEU 45 (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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36C PHE* 5.6 0.7 - - + -
38C GLN* 4.7 0.4 - - - +
44C PRO* 4.0 27.8 - - + -
87C TYR* 3.7 41.4 - - + -
98C PHE* 3.5 54.0 + - + +
99C GLY 5.1 1.2 + - - -
37D VAL* 3.9 17.9 - - + -
38D LYS 3.4 3.1 - - - +
39D GLN* 3.4 32.1 - - + +
43D GLN 3.9 1.8 + - - +
44D GLY* 1.3 71.9 - - - -
46D GLU* 1.3 66.7 + - - +
95D PHE* 4.7 4.0 - - + -
109D TRP* 4.7 1.6 - - + -
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Residues in contact with GLU 46 (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* 4.6 0.4 - - - -
37D VAL* 3.2 8.0 - - - +
38D LYS* 2.7 64.5 + - + +
40D ARG* 4.8 2.1 + - - +
43D GLN* 3.1 41.3 - - - +
44D GLY 5.1 0.9 - - - +
45D LEU* 1.3 80.9 - - - +
47D TRP* 1.3 62.6 + - - +
48D ILE* 3.5 0.9 + - - +
61D ASN* 5.7 1.3 - - - +
63D LYS* 3.5 21.3 + - - +
64D PHE* 3.4 26.8 - - + -
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Residues in contact with TRP 47 (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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94C THR* 3.2 27.1 - - - -
95C PRO* 3.6 23.1 - - + -
96C TRP* 3.6 47.5 + + + +
98C PHE* 4.3 11.8 - - + -
35D HIS* 3.2 21.7 + - + -
36D TRP 3.8 10.3 - - - -
37D VAL* 4.5 4.5 - - + -
46D GLU* 1.3 71.0 - - - +
48D ILE* 1.3 60.6 + - - +
49D GLY* 3.6 22.7 + - - -
50D TRP* 4.0 17.3 - + - -
59D LYS* 4.3 10.3 - - + -
60D TYR 4.1 7.0 - - - -
61D ASN* 2.8 56.1 + - + +
64D PHE* 4.1 1.5 - - - -
106D PHE* 3.8 24.9 - + + -
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Residues in contact with ILE 48 (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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36D TRP* 2.8 20.2 + - + +
37D VAL 4.0 9.0 - - - -
38D LYS* 4.0 6.7 - - + -
46D GLU 4.1 4.5 - - - +
47D TRP* 1.3 74.4 - - - +
49D GLY* 1.3 59.0 + - - +
60D TYR* 3.7 4.9 - - + +
61D ASN* 2.8 27.1 + - - +
64D PHE* 3.9 37.1 - - + +
68D ALA* 3.8 28.9 - - + -
70D LEU* 4.7 3.6 - - + -
81D MET* 3.7 21.3 - - + -
83D LEU* 5.4 0.7 - - + -
94D TYR* 3.7 36.3 - - + -
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Residues in contact with GLY 49 (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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35D HIS* 3.4 2.1 - - - -
36D TRP 2.9 25.3 + - - -
47D TRP* 3.6 20.7 + - - -
48D ILE* 1.3 82.1 - - - +
50D TRP* 1.3 59.3 + - - -
59D LYS 3.1 14.1 - - - -
60D TYR* 4.1 1.1 - - - -
70D LEU* 3.5 13.4 - - - +
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Residues in contact with TRP 50 (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 TRP* 5.3 5.9 - + - -
33D TYR* 3.7 48.5 - + + -
34D ILE 3.1 15.3 - - - +
35D HIS* 3.4 34.3 - + + +
47D TRP* 4.0 13.6 - + - -
49D GLY* 1.3 72.8 - - - -
51D VAL* 1.3 69.4 + - - +
52D PHE* 3.6 5.8 - + + -
57D ASN* 3.2 30.3 - - + -
58D THR* 3.4 16.6 - - - -
59D LYS* 2.9 57.3 + - + +
70D LEU* 3.4 14.2 - - - +
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Residues in contact with VAL 51 (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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33D TYR* 3.4 2.4 - - - -
34D ILE* 2.9 52.2 + - + +
36D TRP* 4.8 5.8 - - - +
50D TRP* 1.3 78.6 - - - +
52D PHE* 1.3 66.1 + - - +
53D PRO* 3.5 2.8 - - + +
56D GLY* 4.2 9.2 - - - +
57D ASN 3.4 11.2 - - - +
58D THR* 4.1 9.6 - - + -
70D LEU* 4.1 11.9 - - + +
71D THR* 4.1 22.9 - - - +
72D ALA* 4.1 14.6 - - + +
79D ALA* 4.0 17.5 - - + -
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Residues in contact with PHE 52 (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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1A ASP* 3.5 33.0 - - + -
95A PRO* 4.2 11.7 - - + -
61B ASN* 4.6 8.1 - - - -
62B GLU* 4.0 18.8 - - + -
63B LYS* 5.2 6.1 - - + -
30D THR 3.1 23.6 - - - -
31D SER 4.2 4.3 - - - -
32D TYR* 3.7 20.0 - - - -
33D TYR* 3.3 34.8 - + + -
50D TRP* 3.6 4.2 - + + -
51D VAL* 1.3 73.9 - - - +
53D PRO* 1.4 70.3 - - + +
55D SER* 3.4 7.6 + - - +
56D GLY* 2.9 26.2 + - - -
57D ASN* 2.8 23.9 + - + +
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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