Contacts of the strand formed by residues 20 - 29 (chain Y) in PDB entry 5FLX
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 20 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E TYR 4.3 5.1 + - - -
55E ALA* 5.0 1.8 - - - +
56E LEU* 5.2 2.0 - - - +
60E GLU* 3.3 28.2 + - - +
15Y ASN* 2.8 34.1 + - + +
18Y LEU* 3.3 43.4 - - + +
19Y GLN* 1.3 78.4 - - - +
21Y LYS* 1.3 66.8 + - - +
22Y GLN* 3.7 25.1 - - + +
74Y MET* 3.4 15.2 - - + +
75Y ILE 3.5 11.0 - - - +
76Y TYR* 3.0 46.9 + - + +
77Y ASP* 5.1 1.3 - - - +
85Y ASN* 4.6 4.0 - - - +
86Y GLU* 3.1 13.7 + - - +
87Y PRO* 6.1 0.4 - - - +
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Residues in contact with LYS 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8401 C 2.6 39.6 + - + +
12Y PHE* 3.4 33.9 - - + -
13Y MET 4.0 4.9 - - - +
14Y THR* 6.0 0.2 - - + -
15Y ASN 4.9 5.4 - - - +
20Y ARG* 1.3 80.9 - - - +
22Y GLN* 1.3 63.9 + - - +
23Y MET* 4.1 7.2 + - + +
48Y TYR* 2.4 44.4 + - - -
74Y MET* 4.4 1.8 - - - -
75Y ILE* 3.1 36.0 + - + +
77Y ASP* 4.2 15.5 + - - +
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Residues in contact with GLN 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LYS* 3.7 12.5 - - - +
54E TYR* 3.3 26.9 + - - +
56E LEU* 4.7 15.2 + - - +
11Y LYS 4.6 0.2 - - - -
12Y PHE* 3.5 1.4 - - - -
13Y MET* 2.6 56.4 + - + +
15Y ASN* 6.0 5.3 - - + +
20Y ARG* 3.7 21.7 - - + +
21Y LYS* 1.3 74.4 - - - +
23Y MET* 1.3 59.3 + - - +
73Y GLY 4.1 4.5 - - - +
74Y MET* 3.6 38.3 - - + +
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Residues in contact with MET 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8371 A 6.0 1.3 - - - -
9Y THR* 3.4 30.7 - - - +
11Y LYS 3.2 8.3 - - - +
12Y PHE* 3.5 33.9 - - + -
21Y LYS* 4.3 9.2 - - + +
22Y GLN* 1.3 77.1 - - - +
24Y VAL* 1.3 61.1 + - - +
25Y ILE* 4.0 20.6 - - + -
44Y LEU* 4.8 8.3 - - - -
48Y TYR* 5.3 8.1 - - + -
72Y PHE* 3.8 4.9 - - - +
73Y GLY* 3.1 34.6 + - - +
75Y ILE* 3.6 31.9 - - + -
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Residues in contact with VAL 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LYS* 4.1 12.3 - - - +
9Y THR* 3.3 3.5 + - - -
10Y ARG* 2.4 50.4 + - + -
11Y LYS* 2.8 40.5 + - + +
23Y MET* 1.3 73.1 - - - +
25Y ILE* 1.3 59.0 + - - +
26Y ASP* 4.2 9.2 - - - +
70Y THR* 4.6 10.1 - - + -
71Y GLY 3.7 8.7 - - - +
72Y PHE* 3.7 29.4 - - + -
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Residues in contact with ILE 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ILE* 3.7 17.9 - - + -
8Y ARG 4.1 3.1 - - - +
9Y THR* 4.8 4.3 - - - +
23Y MET* 4.0 20.6 - - + +
24Y VAL* 1.3 75.5 - - - +
26Y ASP* 1.3 64.0 + - - +
27Y VAL* 3.6 25.1 - - + -
40Y ILE* 5.5 6.5 - - + -
44Y LEU* 3.8 29.2 - - + -
57Y VAL* 4.8 7.4 - - + -
69Y THR 3.3 3.1 - - - +
71Y GLY* 2.6 46.7 + - - +
73Y GLY* 3.7 27.1 - - - +
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Residues in contact with ASP 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y ARG* 2.9 39.9 + - + +
10Y ARG* 2.3 55.2 + - + +
24Y VAL* 4.2 2.9 - - - +
25Y ILE* 1.3 79.0 - - - +
27Y VAL* 1.3 62.0 + - - +
28Y LEU 4.0 1.8 + - - -
63Y HIS* 6.0 0.2 - - - -
68Y LYS* 4.5 21.3 - - + +
69Y THR 3.2 4.3 - - - +
70Y THR* 3.2 32.4 + - - +
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Residues in contact with VAL 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y VAL* 5.1 2.0 - - + -
6Y THR 3.3 19.1 - - - +
7Y ILE* 3.6 30.1 - - + -
25Y ILE* 3.6 23.1 - - + -
26Y ASP* 1.3 71.7 - - - +
28Y LEU* 1.3 60.5 + - - +
29Y HIS* 3.3 33.0 - - + +
40Y ILE* 4.6 17.5 - - + -
60Y PHE* 6.1 2.7 - - + -
68Y LYS* 3.5 2.3 - - - -
69Y THR* 2.9 46.2 + - - +
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Residues in contact with LEU 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y THR 5.0 0.2 - - - +
5Y VAL* 4.6 0.5 - - - -
6Y THR* 3.1 36.0 + - + +
8Y ARG* 3.5 33.3 - - - +
26Y ASP 4.0 2.4 + - - -
27Y VAL* 1.3 72.3 - - - +
29Y HIS* 1.3 81.3 + - - +
30Y PRO* 4.6 2.0 - - - +
67Y GLY* 3.9 23.6 - - - -
68Y LYS* 4.1 14.1 - - + +
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Residues in contact with HIS 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y VAL* 3.9 18.3 - - + +
27Y VAL* 3.3 46.8 + - + +
28Y LEU* 1.3 85.2 + - - +
30Y PRO* 1.3 72.5 - - + +
31Y GLY 3.4 17.8 + - - +
33Y ALA 4.8 8.9 + - - +
34Y THR* 5.3 1.5 - - - +
35Y VAL* 3.3 37.1 + - + +
40Y ILE* 4.9 3.6 - - + +
66Y GLY* 5.3 0.3 - - - -
67Y GLY* 3.5 26.5 + - - +
69Y THR* 3.8 21.1 + - + +
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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