Contacts of the strand formed by residues 13 - 18 (chain D) in PDB entry 3ALQ
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 VAL 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D MET 4.0 6.1 - - - +
12D PRO* 1.3 75.3 - - - +
14D ALA* 1.3 78.8 + - - +
36D LEU* 4.1 19.5 - - + -
37D LEU* 4.5 0.2 - - - -
38D ALA* 3.0 44.1 + - + +
39D ASN* 5.1 0.9 - - - +
41D VAL* 3.3 12.5 - - - +
154D ILE 3.3 13.5 - - - +
155D ILE* 4.2 6.1 - - + -
55E LEU* 3.8 34.1 - - + -
123E VAL* 4.0 20.0 - - + -
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Residues in contact with ALA 14 (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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13D VAL* 1.3 83.1 - - - +
15D HIS* 1.3 61.8 + - - +
16D VAL* 4.0 2.7 - - + -
36D LEU* 3.0 16.6 - - - +
37D LEU* 4.0 9.6 - - + -
41D VAL* 3.9 20.0 - - + -
48D LEU* 4.4 14.1 - - + -
59D TYR* 3.9 4.0 + - - -
153D GLY* 3.0 22.3 - - - -
154D ILE* 2.9 18.0 + - + +
123E VAL* 5.3 0.2 - - - +
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA* 1.3 74.7 - - - +
16D VAL* 1.3 58.7 + - - +
17D VAL* 3.9 14.5 - - + +
34D ASN 3.7 17.0 - - - +
35D ALA* 3.3 8.6 - - - +
36D LEU* 2.7 37.3 + - + +
59D TYR* 2.9 24.6 + + - +
151D TYR* 3.4 42.1 - + + +
152D PHE 3.4 5.1 + - - -
93E LEU 4.8 1.4 + - - -
122E GLY* 4.2 1.8 - - - -
123E VAL* 3.6 19.8 + - + +
124E PHE* 3.7 28.4 - + - -
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Residues in contact with VAL 16 (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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14D ALA* 4.9 0.7 - - + -
15D HIS* 1.3 77.4 - - - +
17D VAL* 1.3 59.4 + - - +
28D TRP* 3.7 25.9 - - + -
29D LEU 3.3 14.1 - - - +
30D ASN* 4.1 10.8 - - + -
36D LEU 4.2 6.3 - - - +
37D LEU* 4.8 4.0 - - + -
43D LEU* 4.0 20.9 - - + -
48D LEU* 4.1 19.1 - - + -
151D TYR* 3.3 5.0 - - - +
152D PHE* 2.8 63.3 + - + +
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Residues in contact with VAL 17 (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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15D HIS* 3.9 25.4 - - + +
16D VAL* 1.3 80.4 - - - +
18D ALA* 1.3 67.7 + - - +
20D PRO* 5.9 0.2 - - + -
28D TRP* 3.6 7.4 - - - -
29D LEU* 2.8 41.2 + - + +
32D ARG* 4.5 23.3 - - + -
34D ASN 5.0 2.2 - - - +
35D ALA* 4.3 8.5 - - + -
148D GLY 6.3 1.3 - - - +
150D VAL 3.5 11.2 - - - +
151D TYR* 4.7 0.7 - - + -
73U SER* 4.5 8.5 - - - +
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Residues in contact with ALA 18 (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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17D VAL* 1.3 80.0 - - - +
19D ASN* 1.3 59.0 - - - +
20D PRO* 3.0 19.5 - - - +
26D LEU* 3.8 10.5 - - + -
27D GLN 3.6 5.6 - - - +
28D TRP* 3.9 2.0 - - - -
144D PHE* 3.7 23.1 - - + +
150D VAL* 3.2 40.9 + - + -
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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