Contacts of the strand formed by residues 30 - 40 (chain A) in PDB entry 1FNA
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 ARG 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A THR* 4.2 21.0 - - - +
29A VAL* 1.3 77.7 + - - +
31A TYR* 1.3 77.8 + - + +
51A PRO* 4.5 1.0 - - - +
52A GLY 3.1 15.1 + - - -
75A VAL* 2.8 17.9 + - + +
76A THR* 4.0 5.3 - - - +
77A GLY* 4.2 27.4 - - - +
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Residues in contact with TYR 31 (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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29A VAL* 3.3 8.7 - - - +
30A ARG* 1.3 100.2 - - + +
32A TYR* 1.3 73.9 - - - +
33A ARG* 3.5 26.3 - - + +
49A THR* 3.7 23.6 - - + -
50A VAL 3.4 13.0 - - - +
51A PRO* 4.8 1.1 - - + -
52A GLY 3.7 4.0 - - - +
75A VAL* 2.8 56.4 + - + +
80A ASP* 5.1 2.9 + - - -
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Residues in contact with TYR 32 (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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22A TRP* 3.3 34.6 + + + -
24A ALA* 3.5 16.6 - - - +
25A PRO* 3.3 24.2 - - + +
29A VAL* 3.8 10.5 - - + +
31A TYR* 1.3 81.1 - - - +
33A ARG* 1.3 61.6 + - - +
34A ILE* 4.0 1.5 + - + -
49A THR* 3.3 8.3 - - - +
50A VAL* 2.8 40.8 + - + +
51A PRO 3.8 10.8 - - - -
52A GLY* 3.7 20.1 + - - -
54A LYS 3.1 26.1 + - - -
72A VAL* 3.7 20.4 - - + -
73A TYR 3.2 12.1 - - - +
74A ALA* 3.9 21.8 - - + -
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Residues in contact with ARG 33 (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 TYR* 3.5 25.8 - - + -
32A TYR* 1.3 72.0 - - - +
34A ILE* 1.3 62.8 - - - +
35A THR* 4.0 5.4 - - + +
47A GLU* 2.9 44.8 + - - +
48A PHE 3.8 4.5 - - - -
49A THR* 4.8 1.6 - - - +
71A THR 3.7 1.0 - - - +
72A VAL* 3.4 4.7 - - - +
73A TYR* 2.9 63.5 + - + -
75A VAL* 4.0 19.5 - - + +
80A ASP* 5.6 4.4 + - - -
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Residues in contact with ILE 34 (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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20A ILE* 3.9 16.8 - - + -
22A TRP* 3.7 17.5 - - + -
32A TYR* 4.0 1.8 + - + +
33A ARG* 1.3 78.7 - - - +
35A THR* 1.3 66.4 + - - +
36A TYR* 4.5 2.8 - - + -
47A GLU* 3.3 5.5 - - - +
48A PHE* 2.9 66.0 + - + -
50A VAL* 3.3 34.5 - - + -
57A ALA* 3.4 15.7 - - + -
59A ILE* 4.2 9.4 - - + -
70A ILE* 4.3 2.7 - - + -
71A THR 3.4 6.7 - - - +
72A VAL* 4.3 13.0 - - + -
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Residues in contact with THR 35 (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 ARG* 5.0 5.4 - - + +
34A ILE* 1.3 78.1 - - - +
36A TYR* 1.3 67.8 - - - +
45A VAL* 3.4 18.4 - - + +
46A GLN 3.2 3.4 - - - -
47A GLU* 4.0 27.1 - - + +
69A THR 3.9 0.4 - - - +
70A ILE* 3.5 3.1 - - - +
71A THR* 2.8 52.6 + - - -
73A TYR* 4.0 22.3 + - + -
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Residues in contact with TYR 36 (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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34A ILE* 4.5 2.2 - - + -
35A THR* 1.3 80.6 - - - +
37A GLY* 1.4 62.2 + - - +
45A VAL* 3.4 5.4 - - - +
46A GLN* 2.8 73.4 + - + +
47A GLU 4.7 0.2 - - - -
48A PHE* 3.7 34.2 - + - -
59A ILE* 3.8 31.3 - - + +
60A SER 4.1 11.1 + - - -
62A LEU* 4.1 17.9 - - + -
68A TYR* 4.5 9.9 - + + -
69A THR 3.2 11.0 - - - +
70A ILE* 4.0 18.8 - - + -
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Residues in contact with GLY 37 (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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36A TYR* 1.4 79.2 - - - +
38A GLU* 1.3 67.7 - - - -
43A SER 6.0 1.6 - - - -
44A PRO 5.5 1.6 - - - -
45A VAL* 4.6 13.9 - - - +
46A GLN* 6.0 0.4 - - - -
68A TYR* 3.3 11.3 - - - -
69A THR* 2.9 34.0 + - - +
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Residues in contact with GLU 38 (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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37A GLY* 1.3 73.0 - - - -
39A THR* 1.3 66.0 + - - +
40A GLY 3.3 0.7 + - - -
41A GLY* 3.0 28.0 + - - +
43A SER* 6.0 7.6 - - - -
63A LYS* 2.7 39.3 + - - +
66A VAL* 4.0 18.4 - - + +
67A ASP 3.6 7.9 - - - +
68A TYR* 3.7 22.0 + - + -
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Residues in contact with THR 39 (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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37A GLY 3.3 1.8 + - - -
38A GLU* 1.3 71.2 - - - +
40A GLY* 1.3 64.0 + - - +
41A GLY* 3.2 0.9 + - - -
67A ASP* 2.6 48.5 + - + +
68A TYR 3.3 6.8 - - - -
69A THR* 2.7 23.8 + - - +
91A ASN* 3.1 11.5 + - - +
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Residues in contact with GLY 40 (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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38A GLU 3.3 0.6 + - - -
39A THR* 1.3 77.3 - - - +
41A GLY* 1.3 63.6 + - - +
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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