Contacts of the strand formed by residues 16 - 26 (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 THR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A THR* 3.1 8.9 + - - -
15A PRO* 1.3 87.8 - - + +
17A SER* 1.3 63.5 + - - +
61A GLY* 3.4 8.2 + - - -
62A LEU* 3.0 48.7 + - - +
64A PRO* 4.1 15.9 - - + -
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Residues in contact with SER 17 (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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13A ALA* 3.5 0.3 - - - -
14A THR* 2.8 47.4 + - - +
16A THR* 1.3 84.1 + - - +
18A LEU* 1.4 64.3 + - - +
58A THR* 4.8 6.9 - - - +
59A ILE 3.1 15.0 - - - -
60A SER* 4.0 12.6 - - - -
62A LEU* 4.2 5.4 - - - +
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Residues in contact with LEU 18 (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 VAL* 4.0 6.1 - - + -
12A ALA 3.4 12.1 - - - +
13A ALA* 4.0 8.1 - - + +
17A SER* 1.4 77.3 + - - +
19A LEU* 1.3 62.1 - - - +
20A ILE* 3.4 33.4 - - + +
58A THR* 3.4 7.0 - - - +
59A ILE* 2.8 52.6 + - + +
62A LEU* 3.6 25.4 - - + -
68A TYR* 5.8 2.2 - - + -
70A ILE* 4.3 13.0 - - + -
92A TYR* 3.9 28.3 - - + -
94A THR* 4.7 2.5 - - + -
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Residues in contact with LEU 19 (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 VAL* 3.5 5.5 - - - -
11A VAL* 2.9 50.5 + - + +
12A ALA* 2.8 28.2 + - + +
18A LEU* 1.3 76.5 - - - +
20A ILE* 1.4 69.6 + - - +
56A THR* 4.2 13.0 - - + +
57A ALA* 3.5 25.8 - - - +
58A THR* 4.1 10.8 - - - +
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Residues in contact with ILE 20 (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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8A LEU* 4.0 17.5 - - + -
9A GLU 3.3 10.1 - - - +
10A VAL* 4.0 13.5 - - + -
11A VAL* 4.9 0.7 - - - -
18A LEU* 3.4 24.4 - - + -
19A LEU* 1.4 73.0 - - - +
21A SER* 1.3 61.1 + - - +
22A TRP* 3.9 13.5 - - + -
34A ILE* 3.9 25.6 - - + -
56A THR* 3.1 8.9 - - - +
57A ALA* 2.9 42.5 + - + +
59A ILE* 4.1 11.7 - - + -
70A ILE* 4.0 29.8 - - + -
72A VAL* 4.5 2.7 - - + -
90A ILE* 4.8 1.8 - - + -
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Residues in contact with SER 21 (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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7A ASP 3.9 1.3 - - - +
8A LEU* 3.4 3.5 - - - +
9A GLU* 2.9 36.1 + - - +
11A VAL* 3.7 24.7 - - - -
20A ILE* 1.3 75.2 - - - +
22A TRP* 1.3 67.2 + - - +
55A SER* 3.4 10.3 + - - -
56A THR* 3.8 15.6 - - - +
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Residues in contact with TRP 22 (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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7A ASP 3.7 7.2 - - - -
8A LEU* 4.1 6.3 - - + -
20A ILE* 3.9 13.2 - - + -
21A SER* 1.3 87.2 + - - +
23A ASP* 1.3 77.4 + - - +
32A TYR* 3.3 53.0 + + + -
34A ILE* 3.7 30.3 - - + -
50A VAL* 4.0 7.0 - - + -
54A LYS 4.0 1.3 - - - -
55A SER* 3.0 52.1 + - - +
56A THR* 3.7 29.2 - - - -
72A VAL* 4.1 22.9 - - + -
88A ILE* 3.7 23.8 - - + -
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Residues in contact with ASP 23 (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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6A ARG* 4.3 15.3 - - - -
7A ASP* 3.1 40.8 + - - +
22A TRP* 1.3 88.8 - - - +
24A ALA* 1.3 70.2 - - - +
25A PRO* 3.7 3.1 - - - +
88A ILE* 4.7 5.9 - - - +
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Residues in contact with ALA 24 (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* 3.9 3.0 + - - -
23A ASP* 1.3 79.9 - - - +
25A PRO* 1.3 74.2 - - + +
29A VAL* 5.8 0.2 - - + -
32A TYR* 3.5 17.0 - - - +
52A GLY 6.0 0.7 - - - +
54A LYS 5.8 0.2 - - - +
55A SER* 4.9 10.6 - - - -
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Residues in contact with PRO 25 (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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23A ASP 3.7 4.9 - - - +
24A ALA* 1.3 93.2 - - + +
26A ALA* 1.3 64.6 + - - +
27A VAL* 3.2 13.4 + - + +
29A VAL* 3.6 22.9 - - + -
32A TYR* 3.3 20.4 - - + +
74A ALA* 4.0 8.5 - - + -
85A SER* 3.7 26.7 - - - +
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Residues in contact with ALA 26 (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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25A PRO* 1.3 76.3 - - - +
27A VAL* 1.3 66.4 + - + +
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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