Contacts of the strand formed by residues 39 - 44 (chain D) in PDB entry 3W13
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D MET* 4.8 1.3 - - + -
23D CYS* 4.6 4.3 - - - -
29D LEU* 4.3 13.7 - - + -
37D ASN 3.1 4.4 + - - -
38D PHE* 1.3 75.7 - - - +
40D ALA* 1.3 75.0 + - - +
41D TRP* 3.5 28.3 - - + +
56D TRP 3.3 7.4 + - - -
57D ALA* 2.9 38.5 + - + -
77D PHE* 4.0 33.9 - - + -
94D CYS* 3.9 15.0 - - + -
95D GLN 3.0 34.8 - - - +
96D GLN* 4.0 3.1 - - - +
97D TYR* 3.4 6.6 - - - -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO* 4.0 9.6 - - + -
39D LEU* 1.3 85.7 - - - +
41D TRP* 1.3 60.5 + - - +
42D TYR* 3.6 26.2 - - + -
52D LEU* 4.8 0.7 - - + -
54D ILE 3.4 9.6 - - - +
94D CYS* 3.4 6.1 - - - -
95D GLN* 2.7 45.9 + - - +
97D TYR* 3.9 8.5 - - + -
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Residues in contact with TRP 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.8 22.9 - - - -
21D MET* 4.3 15.5 - - + -
22D SER 4.4 3.8 - - - -
23D CYS* 3.8 31.2 - - + -
39D LEU* 3.5 25.6 - - + +
40D ALA* 1.3 73.9 - - - +
42D TYR* 1.3 63.9 + - - +
52D LEU* 4.2 1.0 - - - +
53D LEU* 3.2 26.3 + - + +
54D ILE* 2.9 24.0 + - + +
57D ALA* 5.2 5.8 - - - +
70D GLY* 5.1 6.5 - - - -
71D SER 5.0 1.2 + - - -
77D PHE* 4.4 4.3 - - + +
78D THR* 3.8 20.5 + - - -
79D LEU* 3.6 62.1 - - + -
92D TYR* 4.6 3.6 - - + -
93D TYR 3.2 32.1 - - - -
94D CYS* 3.8 6.7 - - + -
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Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 6.3 0.9 - - + -
104C PRO* 3.4 7.4 - - - +
105C MET* 2.5 62.7 + - + +
108C TRP* 3.7 18.4 - + - -
40D ALA* 3.6 20.0 - - + -
41D TRP* 1.3 75.9 - - - +
43D GLN* 1.3 61.1 + - - +
50D PRO* 4.6 9.4 - - + -
51D LYS 3.4 8.7 - - - +
52D LEU* 3.5 31.6 - - + +
53D LEU* 4.2 4.5 - - - -
91D VAL 4.1 0.3 - - - +
92D TYR* 3.3 8.7 - - - +
93D TYR* 3.1 41.4 + - + +
95D GLN* 3.6 17.6 + - + -
103D PHE* 4.1 15.5 - + + -
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 1.3 72.8 - - - +
44D GLN* 1.3 61.3 + - - +
45D LYS* 3.4 42.7 + - - +
50D PRO* 3.4 0.8 - - - +
51D LYS* 2.8 64.7 + - + +
53D LEU* 3.6 16.5 - - + +
68D PHE* 4.5 12.6 - - - -
87D GLU 5.3 0.5 - - - +
88D ASP* 5.2 3.6 - - - +
90D ALA* 3.4 19.5 - - + +
92D TYR* 3.3 30.3 + - + -
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 3.5 27.9 + - - -
45C LEU* 4.2 4.4 - - - +
94C TYR* 4.4 4.8 + - - -
43D GLN* 1.3 75.7 - - - +
45D LYS* 1.3 66.4 + - - +
46D PRO* 3.4 7.9 - - + +
47D GLY 5.3 2.2 - - - +
48D GLN 3.3 25.6 + - - +
50D PRO* 3.7 34.6 - - + +
90D ALA* 3.2 3.3 - - - +
91D VAL* 2.9 45.9 + - - +
93D TYR* 3.6 28.9 + - + -
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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