Contacts of the strand formed by residues 19 - 31 (chain A) in PDB entry 4FK8
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 PHE 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 1.3 95.5 + - + +
20A ASP* 1.3 68.3 + - - +
21A THR* 3.9 2.1 + - - -
54A MET* 3.9 22.2 - - + -
63A PRO* 4.0 28.5 - - + -
65A THR* 3.8 29.6 - - + -
105A LEU* 4.1 26.2 - - + -
106A ILE 3.5 4.5 - - - +
107A GLY* 3.7 21.3 - - - -
108A LYS* 4.1 10.8 - - - +
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Residues in contact with ASP 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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19A PHE* 1.3 74.6 - - - +
21A THR* 1.3 73.7 + - - +
22A ALA* 3.7 20.6 + - - +
40A THR* 4.5 2.3 + - - +
42A ASP* 3.7 38.9 + - + +
45A LEU* 6.3 1.1 - - + -
105A LEU* 3.4 4.5 - - - -
106A ILE* 2.8 45.1 + - + +
108A LYS* 3.5 22.9 + - + +
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Residues in contact with THR 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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19A PHE 3.9 2.6 + - - -
20A ASP* 1.3 81.1 + - - +
22A ALA* 1.3 61.4 + - - +
23A THR* 5.1 1.0 + - - -
103A PRO* 3.7 28.5 - - + -
104A VAL 3.6 6.5 - - - +
105A LEU* 3.7 18.8 - - + +
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Residues in contact with ALA 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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20A ASP* 3.7 8.4 + - - +
21A THR* 1.3 75.8 - - - +
23A THR* 1.3 62.6 + - - +
39A CYS* 4.0 8.5 - - - -
40A THR* 3.4 31.6 - - - +
103A PRO* 3.3 7.8 - - - +
104A VAL* 2.8 36.3 + - + +
106A ILE* 3.8 19.1 - - + -
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Residues in contact with THR 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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21A THR 5.1 1.4 + - - -
22A ALA* 1.3 74.0 + - - +
24A VAL* 1.3 68.1 + - - +
25A LEU* 3.3 8.5 + - + +
39A CYS* 3.2 2.6 - - - -
40A THR* 2.9 42.1 + - - +
101A GLY* 3.7 30.7 - - - +
102A ASP 3.5 2.9 - - - -
103A PRO* 4.7 0.7 - - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 1.3 74.1 - - - +
25A LEU* 1.3 62.3 + - - +
26A SER 3.7 10.3 - - - +
27A VAL* 3.5 30.7 - - + -
37A PHE* 4.3 7.9 - - + -
38A THR 3.6 6.7 - - - +
39A CYS* 4.0 0.9 - - - -
98A LEU* 3.9 34.1 - - + -
99A LYS 3.6 14.4 - - - +
100A VAL* 3.8 3.4 - - - +
101A GLY* 2.8 27.7 + - - -
102A ASP 2.8 21.9 + - - +
104A VAL* 4.0 16.4 - - + -
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Residues in contact with LEU 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 THR* 3.8 15.0 - - + +
24A VAL* 1.3 75.1 - - - +
26A SER* 1.3 60.3 + - - +
38A THR* 2.7 20.4 + - - +
39A CYS* 3.7 20.6 - - - +
40A THR* 3.8 21.8 - - + +
78A HIS* 3.9 20.4 - - + -
100A VAL* 3.6 17.3 - - - +
30B TRP 3.5 13.5 - - - +
31B THR* 4.5 1.0 - - - -
162B LYS* 4.1 24.7 - - + -
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Residues in contact with SER 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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24A VAL* 3.7 1.3 - - - +
25A LEU* 1.3 80.1 - - - +
27A VAL* 1.3 68.6 + - - +
28A HIS* 3.0 22.1 + - - -
37A PHE* 3.3 5.0 - - - +
38A THR* 2.8 48.8 + - - +
100A VAL* 3.9 2.7 - - - -
29B HIS 3.2 15.7 - - - -
30B TRP* 4.0 13.9 - - - -
163B GLY* 6.2 0.4 - - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.5 20.9 - - + -
26A SER* 1.3 81.4 - - - +
28A HIS* 1.3 63.3 + - - +
29A HIS* 5.2 10.1 - - + +
35A PHE* 6.2 2.5 - - + -
36A SER 3.6 6.1 - - - +
37A PHE* 4.1 7.6 - - + -
98A LEU* 3.7 32.1 - - + +
99A LYS* 4.2 4.3 - - - -
100A VAL* 4.3 7.2 - - + +
27B VAL 4.2 0.6 - - - +
28B HIS* 3.5 0.7 - - - -
29B HIS* 2.8 62.4 + - + -
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Residues in contact with HIS 28 (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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26A SER* 3.0 29.3 + - - -
27A VAL* 1.3 79.2 - - - +
29A HIS* 1.3 65.0 + - - +
30A TRP* 3.4 27.2 - + - +
35A PHE* 3.1 7.4 - - - +
36A SER* 2.9 46.8 + - - +
37A PHE* 4.7 2.0 - - - -
38A THR* 5.1 3.8 - - + +
80A GLU* 5.7 2.2 - - - -
170A TYR* 5.6 7.5 + + - -
27B VAL 3.5 4.5 - - - -
28B HIS* 2.8 29.4 + - + +
29B HIS 4.7 0.9 - - - -
30B TRP* 3.6 43.6 - + - -
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Residues in contact with HIS 29 (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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27A VAL* 5.2 11.8 - - + +
28A HIS* 1.3 75.2 - - - +
30A TRP* 1.3 62.1 + - - +
31A THR 3.6 0.7 - - - -
34A LEU 3.8 2.5 - - - -
35A PHE* 3.6 15.9 - + + +
85A LYS* 2.9 31.3 + - - +
96A GLN* 3.2 28.0 + - + -
98A LEU 5.2 5.1 + - - -
26B SER* 3.2 10.6 - - - -
27B VAL* 2.8 45.4 + - + +
28B HIS* 4.5 0.4 + - - -
29B HIS* 5.5 3.1 - + - -
99B LYS* 6.6 0.4 - - - -
100B VAL* 3.8 20.3 - - + +
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Residues in contact with TRP 30 (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 HIS* 3.4 25.7 - + + +
29A HIS* 1.3 73.9 - - - +
31A THR* 1.3 67.7 + - + +
34A LEU* 3.0 17.0 + - + +
35A PHE* 4.4 1.3 - - - -
36A SER* 2.9 29.7 + - - -
82A PHE* 4.8 4.0 - + + -
163A GLY* 3.6 27.9 - - - +
164A GLU* 5.6 0.4 - - - -
166A ALA* 4.0 24.7 - - + -
167A TYR* 3.2 42.4 - + + -
170A TYR* 3.9 33.7 - + + -
25B LEU 3.4 14.7 - - - +
26B SER* 4.0 7.5 - - - -
28B HIS* 3.6 29.2 - + - -
30B TRP* 6.1 2.2 - + - -
170B TYR* 5.4 10.5 - + - -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 1.3 85.0 + - + +
32A ASP* 1.3 63.2 + - - +
33A THR* 3.1 20.6 + - - -
34A LEU* 3.2 20.4 + - + +
85A LYS* 3.0 21.8 + - - -
161A LEU* 4.8 15.4 - - + +
163A GLY* 3.7 26.7 - - - +
164A GLU* 4.0 13.9 - - + +
25B LEU 4.6 0.9 - - - -
100B VAL* 4.0 16.0 - - - +
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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