Contacts of the strand formed by residues 39 - 44 (chain L) in PDB entry 4WEB
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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4L MET* 3.5 30.7 - - + -
23L CYS* 3.7 13.0 - - - -
29L LEU* 3.7 14.8 - - + -
37L ASN 2.9 6.7 + - - -
38L TYR* 1.3 75.1 - - - +
40L ALA* 1.3 64.1 + - - +
41L TRP* 3.3 37.2 - - + +
54L VAL* 4.2 0.5 - - - +
55L TYR* 3.5 1.2 - - - -
56L PHE 3.2 6.9 + - - -
57L ALA* 2.8 32.5 + - - +
77L PHE* 3.7 41.7 - - + -
94L CYS* 4.2 2.7 - - + -
95L GLN 3.6 7.4 - - - +
97L HIS* 3.5 1.8 + - - -
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Residues in contact with ALA 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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104H ALA* 4.5 2.2 - - + -
39L LEU* 1.3 75.4 - - - +
41L TRP* 1.3 64.5 + - - +
42L TYR* 3.7 30.5 - - + +
52L LEU* 4.2 4.9 - - + -
54L VAL 3.2 10.8 - - - +
55L TYR* 4.4 1.8 - - - -
93L PHE 3.9 0.2 - - - +
94L CYS* 3.2 7.6 - - - +
95L GLN* 2.8 35.0 + - - +
97L HIS* 3.7 17.3 - - + +
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Residues in contact with TRP 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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6L GLN* 3.5 24.2 - - - -
21L MET* 4.2 13.9 - - + -
22L SER 4.0 12.6 - - - -
23L CYS* 3.4 33.2 - - + -
39L LEU* 3.3 23.7 - - + +
40L ALA* 1.3 74.5 - - - +
42L TYR* 1.3 61.7 + - - +
52L LEU* 3.7 3.3 - - - +
53L LEU* 2.8 29.2 + - + -
54L VAL* 2.8 40.1 + - + +
57L ALA 4.8 2.5 + - - -
70L GLY* 4.7 3.7 - - - -
71L SER 5.4 0.2 + - - -
77L PHE* 4.8 0.6 - - - +
78L THR* 3.8 16.1 + - - -
79L LEU* 3.5 56.8 - - + +
92L TYR* 5.0 1.6 - - + -
93L PHE 3.4 20.9 - - - -
94L CYS* 3.6 7.9 - - + -
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Residues in contact with TYR 42 (chain L).
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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45H LEU* 5.3 0.9 - - + -
104H ALA* 3.7 3.5 - - - -
105H LEU* 2.7 53.5 + - + +
108H TRP* 3.8 17.7 - + - -
40L ALA* 3.7 11.6 - - + +
41L TRP* 1.3 75.8 - - - +
43L GLN* 1.3 60.5 + - - +
50L PRO* 4.5 11.7 - - + -
51L LYS 3.3 6.5 - - - +
52L LEU* 3.6 29.2 - - + -
53L LEU* 4.2 4.0 - - - -
91L ASP 3.9 0.3 - - - +
92L TYR* 3.2 8.7 - - - +
93L PHE* 2.7 54.4 + - + +
95L GLN* 2.6 43.6 + - + -
104L PHE* 3.8 15.3 - + - -
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Residues in contact with GLN 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 76.5 - - - +
44L GLN* 1.3 63.8 + - - +
45L LYS* 3.7 20.5 + - + +
49L SER 4.1 0.9 - - - +
50L PRO* 3.4 1.0 - - - +
51L LYS* 2.8 51.5 + - + +
53L LEU* 3.5 25.9 - - + +
68L PHE* 4.0 4.2 - - - -
88L ASP 3.9 5.5 + - - -
90L ALA* 3.6 11.0 - - + +
91L ASP 3.7 2.2 - - - -
92L TYR* 2.9 31.6 + - + -
302L ARF 3.0 42.5 + - - -
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Residues in contact with GLN 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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39H GLN* 2.8 44.4 + - - -
95H TYR* 3.3 9.5 + - - -
43L GLN* 1.3 76.0 - - - +
45L LYS* 1.3 64.1 + - - +
46L PRO* 3.8 1.7 - - + +
47L GLY 5.9 0.2 - - - +
48L GLN 3.1 27.5 + - - +
49L SER 4.1 1.1 - - - -
50L PRO* 3.6 26.8 - - + +
90L ALA* 3.5 4.1 - - - -
91L ASP* 2.8 45.7 + - + +
93L PHE* 3.5 19.2 - - + -
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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