Contacts of the strand formed by residues 51 - 61 (chain K) in PDB entry 4FAO
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 51 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K ARG 4.6 0.2 - - - -
47K ASN* 3.7 2.1 - - - +
48K SER* 2.8 45.4 + - - -
49K SER 3.3 4.0 + - - +
50K GLY* 1.3 75.4 - - - +
52K ILE* 1.3 60.8 + - - +
53K GLU* 3.7 3.5 + - - +
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Residues in contact with ILE 52 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45K TRP* 3.7 34.3 - - + +
46K ARG 3.7 3.1 - - - -
47K ASN* 3.4 16.2 - - - +
50K GLY 3.6 9.4 + - - +
51K THR* 1.3 70.9 - - - +
53K GLU* 1.3 63.3 + - - +
54K LEU* 4.0 2.5 + - - +
95K PHE* 4.2 18.2 - - + -
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Residues in contact with GLU 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ALA* 5.6 3.0 - - + +
45K TRP* 3.4 3.6 - - - +
46K ARG* 2.8 72.0 + - + +
48K SER* 6.1 0.9 - - - +
51K THR 3.7 2.9 + - - +
52K ILE* 1.3 73.1 - - - +
54K LEU* 1.3 72.2 + - - +
55K VAL* 4.0 2.3 - - - +
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Residues in contact with LEU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K TYR* 3.9 36.9 + - + +
16K ALA* 3.5 16.7 - - - +
44K SER 3.3 16.8 - - - +
45K TRP* 4.0 6.7 - - + -
52K ILE* 4.0 4.0 + - + +
53K GLU* 1.3 82.6 - - - +
55K VAL* 1.3 72.4 + - - +
56K LYS* 3.8 8.1 - - - +
57K LYS* 3.6 42.8 - - + +
95K PHE* 4.6 13.9 - - + -
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Residues in contact with VAL 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G PRO* 4.1 31.6 - - + +
14K TYR* 4.6 1.1 - - - -
15K ASN* 3.9 1.4 - - - +
16K ALA* 3.3 24.9 + - + +
17K ASN* 4.5 1.1 + - + -
44K SER* 3.0 23.7 + - - +
45K TRP* 4.2 0.9 - - - -
46K ARG* 3.9 43.3 - - + +
53K GLU* 3.7 10.7 + - - +
54K LEU* 1.3 80.6 - - - +
56K LYS* 1.3 79.5 + - + +
81K VAL* 5.5 4.5 - - + -
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Residues in contact with LYS 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G LEU* 4.3 12.8 - - + -
93G PRO 3.1 20.8 + - - +
94G THR* 4.1 8.5 - - - +
95G LEU* 4.6 7.6 - - + +
13K TYR* 6.0 0.4 - - - -
14K TYR* 3.2 13.0 - - - +
15K ASN* 2.6 32.8 + - + +
17K ASN* 4.0 4.9 - - - +
21K GLU* 2.9 32.9 + - - -
42K TYR* 3.8 22.2 - - + +
43K ALA* 3.3 2.1 - - - -
44K SER* 2.8 46.6 + - - +
54K LEU* 3.8 2.7 - - - +
55K VAL* 1.3 91.0 + - + +
57K LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ILE* 3.2 30.5 - - + +
13K TYR* 3.5 7.4 - - - -
14K TYR* 2.7 39.1 + - + +
42K TYR* 3.3 14.5 + - - +
43K ALA* 3.9 11.7 - - + -
54K LEU* 3.6 30.1 - - + +
56K LYS* 1.3 78.3 - - - +
58K GLY* 1.3 58.4 + - - +
92K ASN* 3.4 20.8 + - - +
93K GLU* 3.2 22.5 + - - +
95K PHE* 4.1 20.0 - - - -
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Residues in contact with GLY 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K CYS* 4.0 7.0 - - - -
12K ILE 3.1 14.4 + - - -
13K TYR* 4.4 3.1 - - - -
29K GLU* 3.8 7.9 - - - -
41K CYS* 3.4 4.2 - - - -
42K TYR* 2.9 44.0 + - - -
57K LYS* 1.3 75.3 - - - +
59K CYS* 1.3 63.4 + - - -
92K ASN* 3.8 1.0 + - - -
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Residues in contact with CYS 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 4.3 5.2 - - - +
97G TYR* 3.8 27.3 - - + +
11K CYS* 3.8 6.7 - - - -
29K GLU* 2.8 44.4 + - - +
31K CYS* 2.0 54.7 - - + -
40K HIS 3.6 4.3 - - - -
42K TYR* 3.4 13.2 - - - -
58K GLY* 1.3 75.8 - - - -
60K TRP* 1.3 59.0 + - - +
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Residues in contact with TRP 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ALA 3.5 19.5 - - - -
29G PRO* 3.8 15.0 - - + -
83G SER* 3.4 38.1 - - - +
84G VAL* 3.8 4.0 - - - -
85G LEU* 3.9 16.6 - - + -
95G LEU* 4.2 10.1 - - + -
97G TYR* 3.8 8.5 - - - -
39K LEU* 3.9 2.9 - - - +
40K HIS* 2.9 45.5 + - + +
41K CYS 4.3 0.4 - - - -
42K TYR* 4.1 28.0 - + + -
59K CYS* 1.3 75.8 - - - +
61K LEU* 1.3 69.9 + - - +
63K ASP* 3.2 28.2 + - + +
66K CYS* 3.9 22.6 - - - -
83K PHE* 3.7 35.0 - + - -
85K CYS* 4.4 0.4 - - + -
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Residues in contact with LEU 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G PRO* 4.2 25.6 - - + +
82G ILE* 4.4 5.3 - - - +
83G SER* 3.3 26.0 + - - +
97G TYR* 3.2 50.0 - - + +
98G HIS* 4.1 18.2 - - + +
32K GLU 4.2 3.8 - - - +
33K GLY* 4.8 4.5 - - - -
34K GLU 5.5 1.1 - - - +
38K ARG 4.9 0.7 - - - +
39K LEU* 3.7 18.8 - - + -
40K HIS* 3.7 2.0 - - - -
60K TRP* 1.3 79.7 + - - +
62K ASP* 1.3 57.5 - - + +
63K ASP* 2.5 31.8 + - - +
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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