Contacts of the strand formed by residues 39 - 48 (chain L) 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 LEU 39 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97H TYR* 4.5 1.1 - - - +
9L ARG* 3.0 50.8 + - + -
31L CYS* 3.6 29.4 - - + +
32L GLU 4.1 4.3 - - - +
33L GLY* 3.9 20.4 - - - -
34L GLU 5.2 0.9 - - - +
37L LYS 4.6 6.1 - - - +
38L ARG* 1.3 82.0 - - - +
40L HIS* 1.3 72.6 + - - +
60L TRP 4.1 2.9 - - - +
61L LEU* 3.7 26.0 - - + -
87L GLU* 3.7 10.1 + - - +
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Residues in contact with HIS 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ARG* 3.6 3.6 - - - +
11L CYS* 3.4 9.4 - - - -
31L CYS* 4.4 2.1 - - - -
38L ARG* 3.9 8.3 - - - +
39L LEU* 1.3 82.6 + - - +
41L CYS* 1.3 66.5 + - - +
59L CYS* 3.6 1.6 - - - +
60L TRP* 2.9 42.3 + - + +
61L LEU 3.7 2.2 - - - -
62L ASP* 3.4 29.3 - - - -
63L ASP 3.4 22.7 + - - -
66L CYS* 2.9 39.1 + - + +
67L TYR* 3.7 19.1 - + - -
86L CYS 3.2 14.1 + - - +
87L GLU* 4.2 10.4 - - - +
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Residues in contact with CYS 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ARG* 4.4 4.5 - - - -
10L GLU 3.7 10.5 - - - -
11L CYS* 2.0 46.4 - - - -
40L HIS* 1.3 75.9 - - - +
42L TYR* 1.3 59.9 + - - +
58L GLY 3.4 1.3 - - - -
60L TRP* 4.4 1.6 - - - -
85L CYS* 3.0 6.6 - - - +
86L CYS* 2.9 33.9 + - - -
88L GLY 4.0 6.1 - - - -
90L PHE 4.4 1.8 - - - -
91L CYS* 3.6 24.0 - - - -
92L ASN* 3.6 20.2 - - - +
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Residues in contact with TYR 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 5.0 7.6 - - + -
95H LEU* 3.0 31.3 - - + +
13L TYR* 5.6 2.8 - - - -
14L TYR 5.1 0.2 + - - -
41L CYS* 1.3 75.0 - - - +
43L ALA* 1.3 68.3 + - - +
44L SER* 4.3 4.3 - - - -
56L LYS* 3.7 39.3 - - + +
57L LYS* 3.3 6.6 + - - -
58L GLY* 2.9 65.5 + - - -
59L CYS 3.5 15.5 - - - -
60L TRP* 4.1 16.4 - + + -
72L CYS* 4.8 0.2 - - - -
83L PHE* 3.8 31.6 - + + -
84L CYS 3.1 11.2 - - - +
85L CYS* 4.5 0.4 - - + -
92L ASN* 2.8 24.1 + - - -
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Residues in contact with ALA 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L TYR* 1.3 78.2 - - - +
44L SER* 1.3 63.1 + - - +
45L TRP* 3.6 11.1 - - + -
54L LEU* 5.4 0.2 - - + -
56L LYS 3.3 8.3 - - - -
57L LYS* 3.8 20.0 - - + -
72L CYS* 4.2 3.8 - - - -
83L PHE* 3.5 2.4 - - - -
84L CYS* 2.9 46.2 + - - +
92L ASN* 4.4 4.0 - - + -
95L PHE* 4.5 11.2 - - + -
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Residues in contact with SER 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 4.0 26.4 - - - +
42L TYR* 4.3 2.4 - - - -
43L ALA* 1.3 77.2 - - - +
45L TRP* 1.3 63.1 + - - +
54L LEU* 3.2 4.7 - - - +
55L VAL* 2.9 27.1 + - - +
56L LYS* 2.9 31.3 + - - +
81L VAL* 4.1 4.7 - - - -
82L TYR 3.0 16.8 - - - -
83L PHE* 4.3 4.7 - - - -
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Residues in contact with TRP 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ALA* 3.6 20.6 - - + -
44L SER* 1.3 85.0 - - - +
46L ARG* 1.3 73.3 + - - +
47L ASN* 4.7 4.9 + - + +
52L ILE* 3.7 17.2 - - + +
53L GLU 3.3 15.3 - - - +
54L LEU* 4.0 7.4 - - + -
55L VAL* 3.9 6.7 - - - +
74L ALA* 3.9 21.8 - - + -
81L VAL* 3.8 3.8 - - - +
82L TYR* 2.8 66.2 + + + +
83L PHE 4.4 0.4 - - - -
84L CYS* 3.9 14.6 - - + -
95L PHE* 3.0 50.0 - + + -
96L THR* 3.9 18.4 - - - -
97L HIS* 5.0 2.5 - - + +
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Residues in contact with ARG 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H GLY 4.3 7.1 + - - -
92H VAL* 5.2 3.2 - - - +
93H PRO* 3.5 34.1 - - - +
45L TRP* 1.3 84.8 - - - +
47L ASN* 1.3 61.5 + - - +
48L SER 4.1 1.1 - - - +
51L THR 4.6 0.2 - - - -
52L ILE* 3.7 2.1 - - - -
53L GLU* 2.8 58.1 + - + +
55L VAL* 3.9 24.1 - - + +
80L GLN 4.0 17.7 - - - +
81L VAL* 4.8 9.6 - - + +
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Residues in contact with ASN 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L TRP* 4.7 3.4 + - + -
46L ARG* 1.3 75.3 - - - +
48L SER* 1.3 58.7 + - - +
49L SER* 3.2 8.1 + - - +
50L GLY* 3.5 23.3 - - - +
51L THR 3.7 6.3 - - - +
52L ILE* 3.4 27.9 - - - +
80L GLN 4.7 2.6 + - - -
82L TYR* 3.4 48.6 + - + -
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Residues in contact with SER 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ARG* 4.1 2.3 - - - +
47L ASN* 1.3 70.1 - - - +
49L SER* 1.3 69.9 + - - +
50L GLY 3.5 0.2 - - - -
51L THR* 2.7 37.6 + - - +
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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