Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 3DGG
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 LEU 45 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 5.7 0.4 - - + -
42C GLN* 4.6 0.4 - - - +
48C PRO* 3.9 28.7 - - + -
91C TYR* 3.8 31.9 - - + -
101C PHE* 3.7 60.6 + - + +
102C GLY 5.2 1.2 + - - -
37D VAL* 4.0 20.2 - - + -
38D LYS 3.7 2.2 - - - -
39D GLN* 3.8 33.4 - - + +
44D GLY* 1.3 73.5 - - - -
46D GLU* 1.3 60.2 + - - +
47D TRP 4.2 0.4 + - - -
95D TYR* 4.7 3.1 - - + -
109D TRP* 4.8 1.1 - - + -
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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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37D VAL* 3.3 6.6 - - - +
38D LYS* 2.8 56.7 + - + +
44D GLY 5.4 0.4 - - - +
45D LEU* 1.3 73.6 - - - +
47D TRP* 1.3 72.4 + - - +
48D ILE* 3.7 0.9 - - - +
61D ASN* 4.0 8.0 + - - +
63D LYS* 4.2 4.5 - - - +
64D PHE* 3.6 32.5 + - + -
456D MG 3.2 26.5 - - - -
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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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31A THR 4.0 6.3 - - - -
98C LEU* 5.4 11.2 - - + -
99C LEU* 3.5 56.1 - - + +
100C THR* 5.7 0.6 - - - +
101C PHE* 5.0 10.6 - - + -
35D HIS* 3.2 18.1 + - + -
36D TRP 3.6 11.0 - - - -
37D VAL* 4.5 4.5 - - + +
45D LEU 4.2 0.8 + - - -
46D GLU* 1.3 77.5 - - - +
48D ILE* 1.3 66.2 + - - +
49D GLY* 3.3 28.7 + - - -
50D TYR* 4.1 14.4 - + - -
59D ASN* 4.0 20.6 - - - -
60D TYR 4.2 3.4 - - - -
61D ASN* 2.8 68.2 + - + +
64D PHE* 4.6 0.5 - - - +
106D TRP* 3.9 20.0 - + - -
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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* 2.9 33.0 + - + +
37D VAL 3.9 1.8 - - - +
38D LYS* 3.5 27.4 - - + +
46D GLU 3.7 5.2 - - - +
47D TRP* 1.3 74.6 - - - +
49D GLY* 1.3 61.0 + - - +
60D TYR* 3.4 10.4 - - + +
61D ASN* 2.8 25.9 + - - +
64D PHE* 3.1 50.0 - - + +
68D ALA* 3.8 28.7 - - + -
70D LEU* 5.1 3.1 - - + -
81D MET* 4.2 15.3 - - - -
94D TYR* 4.9 2.2 - - + -
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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 0.7 - - - -
36D TRP 2.8 25.6 + - - -
47D TRP* 3.3 23.2 + - - +
48D ILE* 1.3 82.3 - - - +
50D TYR* 1.3 60.6 + - - -
59D ASN 3.0 14.8 - - - -
60D TYR* 4.0 0.2 - - - -
70D LEU* 3.4 13.2 - - - +
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Residues in contact with TYR 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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30A SER* 2.6 24.0 + - - -
31A THR 3.4 17.0 - - - -
33A GLY* 3.4 30.6 + - - -
33D VAL* 3.5 19.1 - - + -
34D MET 3.1 13.5 - - - +
35D HIS* 3.5 18.8 - + - +
47D TRP* 4.1 8.3 - + - -
49D GLY* 1.3 73.7 - - - -
51D ILE* 1.3 66.2 + - - +
52D ASN* 4.1 9.0 - - + -
57D ASP* 4.0 19.7 - - + +
58D THR* 3.3 12.7 + - - -
59D ASN* 2.9 59.8 + - + +
70D LEU* 3.5 8.3 - - - +
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Residues in contact with ILE 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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29D PHE* 6.4 0.2 - - + -
33D VAL* 3.7 0.7 - - - +
34D MET* 3.0 46.7 + - + +
36D TRP* 5.0 4.3 - - - +
50D TYR* 1.3 76.7 - - - +
52D ASN* 1.3 67.8 + - - +
53D PRO* 3.3 5.4 - - + +
56D ASP* 4.4 13.0 - - + +
57D ASP 3.4 9.4 - - - +
58D THR* 3.9 9.4 - - + -
70D LEU* 3.7 15.4 - - + +
71D THR* 3.3 46.7 - - - +
72D SER* 3.5 21.5 - - - +
79D ALA* 4.4 7.2 - - + -
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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