Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 3EYF
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
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Residue Dist Surf HB Arom Phob DC
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36C TYR* 6.1 1.6 - - + -
38C HIS* 5.4 2.0 - - + +
44C PRO* 4.7 9.2 - - + -
87C TYR* 3.8 39.7 - - + -
99C PHE* 3.7 42.2 - - + +
100C GLY 5.0 2.5 + - - +
37D VAL* 3.8 14.1 - - + -
38D ARG 3.5 3.4 - - - +
39D GLN* 3.8 31.2 - - + +
44D GLY* 1.3 74.4 - - - +
46D GLN* 1.3 62.0 + - - +
95D TYR* 3.9 17.0 - - + -
115D TRP* 4.4 15.5 - - + -
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Residues in contact with GLN 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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99C PHE* 4.7 0.4 - - - -
37D VAL* 3.8 3.3 - - - +
38D ARG* 2.6 70.0 + - + +
44D GLY 5.6 0.2 - - - +
45D LEU* 1.3 75.1 - - - +
47D TRP* 1.3 75.9 + - - +
48D LEU* 3.7 6.4 - - + +
61D THR* 4.5 11.7 + - - +
63D SER* 4.2 16.4 + - - -
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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 TRP* 4.2 7.4 - + - -
95C PRO* 3.8 17.5 - - + -
96C PRO* 4.0 14.9 - - + +
97C VAL* 3.5 55.4 + - + +
99C PHE* 4.2 9.1 - - + -
35D HIS* 2.9 30.7 + + + -
36D TRP 3.9 10.3 - - - -
37D VAL* 4.0 15.1 - - + +
46D GLN* 1.3 89.3 - - - +
48D LEU* 1.3 62.6 + - - +
49D THR* 3.5 31.6 + - - -
50D VAL* 3.8 15.0 - - + -
59D ARG* 3.9 12.1 - - + -
60D TYR 3.9 0.9 - - - -
61D THR* 3.5 37.0 + - - +
112D LEU* 4.9 2.0 - - + -
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Residues in contact with LEU 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* 3.0 33.8 + - + +
37D VAL 4.1 0.4 - - - -
38D ARG* 3.4 61.9 - - + +
46D GLN* 3.7 9.4 - - + +
47D TRP* 1.3 87.5 - - - +
49D THR* 1.3 70.1 + - + +
60D TYR* 3.4 0.9 - - - -
61D THR* 2.8 35.2 + - + +
64D VAL* 4.0 17.5 - - + +
68D PHE* 5.0 5.2 - - + -
81D LEU* 5.6 0.4 - - + -
94D TYR* 4.0 14.8 - - + -
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Residues in contact with THR 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* 3.2 3.6 - - - -
36D TRP* 2.9 42.6 + - + -
47D TRP* 3.5 13.7 + - - -
48D LEU* 1.3 86.4 - - + +
50D VAL* 1.3 70.4 + - - +
59D ARG 2.4 25.0 + - - -
60D TYR* 3.2 24.8 - - + -
68D PHE* 5.3 3.1 - - + -
70D ILE* 3.6 19.2 - - + +
81D LEU* 4.3 14.1 - - + -
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Residues in contact with VAL 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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94C TRP* 3.8 18.6 - - + -
33D GLY 4.6 0.2 - - - -
34D ILE 3.4 19.1 - - - +
35D HIS* 3.4 32.1 - - + +
47D TRP* 3.9 2.2 - - + -
49D THR* 1.3 84.6 + - - +
51D ILE* 1.3 68.7 + - - +
58D GLU* 3.4 2.9 - - - -
59D ARG* 2.9 50.8 + - + +
70D ILE* 3.8 4.0 - - - +
108D TYR* 3.7 29.8 - - + -
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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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33D GLY* 3.3 2.1 - - - -
34D ILE* 3.0 33.0 + - + +
50D VAL* 1.3 79.1 - - - +
52D SER* 1.3 68.6 + - - +
55D GLY* 4.1 15.3 - - - +
57D ASP 3.4 11.9 - - - +
58D GLU* 4.2 8.1 - - + +
70D ILE* 3.7 28.5 - - + +
71D SER* 3.7 33.0 - - - +
72D ARG* 3.8 27.6 - - + +
79D MET* 3.9 14.8 - - + -
108D TYR* 3.8 2.9 - - - -
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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