Contacts of the strand formed by residues 44 - 52 (chain A) in PDB entry 3FDR
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 TRP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.1 12.1 - - - +
14A MET* 3.9 35.2 - - + +
15A THR* 3.0 23.3 + - + -
18A TYR* 3.3 37.0 - + + -
19A GLU* 3.8 15.5 - - - +
20A ASN 5.6 0.4 - - - -
35A ALA* 3.7 11.0 - - + -
36A ALA 3.3 22.2 - - - -
37A PRO* 3.6 31.9 - - + +
42A GLY 4.0 8.7 + - - -
43A SER* 1.3 77.1 - - - +
45A TYR* 1.3 69.3 + - - +
75A ASP 3.4 19.3 - - - -
77A ARG* 3.5 37.7 - - + -
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.9 16.2 - - + +
14A MET* 3.5 8.5 - - - -
35A ALA* 3.3 5.0 - - - -
36A ALA* 2.8 34.3 + - - +
38A LEU* 3.5 38.5 - - + +
41A ASN* 2.7 26.4 + - - -
43A SER* 3.3 28.1 + - - -
44A TRP* 1.3 77.8 - - - +
46A ARG* 1.3 63.6 + - - +
62A PHE* 3.7 29.4 - + + -
64A ASP* 5.8 0.7 - - + -
65A PHE* 3.1 46.6 - + + -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.5 17.6 - - + +
14A MET* 3.6 21.5 - - + -
33A ILE* 4.8 2.7 - - + -
34A VAL 3.6 6.5 - - - +
45A TYR* 1.3 74.1 - - - +
47A ALA* 1.3 59.3 + - - +
62A PHE* 3.7 6.8 - - - -
63A VAL* 3.3 33.9 + - + +
64A ASP* 2.8 42.9 + - - +
79A LEU* 4.0 17.3 - - + -
83A PHE 2.9 30.5 + - - -
84A LEU* 3.6 10.3 - - - +
86A LEU* 2.7 36.0 + - - +
87A PRO 3.2 12.7 + - - -
88A PHE* 3.6 16.6 - - - -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.3 5.9 - - - +
34A VAL* 2.8 51.1 + - + +
36A ALA* 4.2 5.2 - - + -
46A ARG* 1.3 75.7 - - - +
48A ARG* 1.3 58.7 - - - +
60A LEU* 4.1 24.2 - - + -
61A TYR 3.3 9.9 - - - +
62A PHE* 4.1 16.4 - - + -
63A VAL* 4.4 3.4 - - - +
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 4.0 18.9 + - - +
32A ASP 3.4 9.4 - - - +
33A ILE* 3.9 15.7 - - + +
47A ALA* 1.3 72.4 - - - +
49A VAL* 1.3 72.7 + - - +
50A LEU* 3.4 12.6 + - + +
60A LEU* 3.4 3.6 - - - -
61A TYR* 2.9 53.8 + - + +
63A VAL* 3.8 23.9 - - + +
88A PHE* 3.8 24.0 - - - -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.8 10.1 - - + -
29A HIS 3.9 20.6 - - - +
30A VAL* 3.6 7.3 - - + +
31A GLY* 2.9 27.2 + - - -
32A ASP* 2.9 22.6 + - + +
34A VAL* 3.9 30.5 - - + -
48A ARG* 1.3 73.9 - - - +
50A LEU* 1.3 61.4 + - - +
51A GLY* 3.8 17.3 - - - +
58A LEU* 4.3 19.3 - - + -
59A ASP 3.8 7.4 - - - +
60A LEU* 4.2 8.5 - - + -
76A LEU* 4.8 0.7 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.6 18.5 - - + +
48A ARG* 4.1 13.5 - - - +
49A VAL* 1.3 78.2 - - - +
51A GLY* 1.3 59.3 + - - +
59A ASP* 2.8 34.5 + - - +
60A LEU 3.7 19.7 - - - +
61A TYR* 3.8 24.5 - - + +
68A ASN* 3.8 21.3 - - - +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.7 17.0 - - - +
49A VAL* 3.6 5.4 - - - +
50A LEU* 1.3 80.5 - - - +
52A THR* 1.3 62.6 + - - -
58A LEU* 3.5 12.5 - - - +
59A ASP* 2.9 25.3 + - - +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY* 1.3 74.8 - - - -
53A LEU* 1.3 76.5 + - - +
56A GLY* 3.7 25.8 - - - +
57A ASN 3.6 4.7 - - - +
58A LEU* 4.1 11.6 - - + +
59A ASP* 4.8 0.9 - - - -
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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