Contacts of the strand formed by residues 30 - 36 (chain U) in PDB entry 1W13
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 PHE 30 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U ILE* 3.8 17.7 - - + +
27U GLN* 3.0 24.5 + - + +
28U PRO 3.4 2.0 - - - +
29U TRP* 1.3 83.3 - - + +
31U ALA* 1.3 72.8 + - - +
32U ALA* 4.2 3.1 - - + -
40U TYR* 3.5 22.2 - - - -
43U GLY* 3.9 16.2 - - - -
44U GLY 3.6 11.2 - - - -
67U TYR 4.3 2.4 - - - +
68U LEU* 4.0 11.8 - - - +
69U GLY 4.5 1.2 + - - -
70U ARG 4.9 2.4 + - - -
139U THR* 3.8 28.9 - - + -
140U GLY* 4.2 5.8 - - - -
141U PHE* 3.7 26.9 - + - -
155U LEU* 3.8 20.6 - - + -
197U GLY* 4.6 0.9 - - - -
198U PRO* 3.8 15.5 - - + -
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Residues in contact with ALA 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U TRP 3.5 2.0 + - - +
30U PHE* 1.3 79.7 - - - +
32U ALA* 1.3 60.1 + - - +
33U ILE* 4.0 1.5 + - + -
43U GLY* 3.5 6.8 - - - -
44U GLY* 2.9 43.3 + - - +
45U SER* 4.3 1.1 - - - +
52U VAL* 4.0 19.7 - - + -
66U VAL* 4.2 9.4 - - + -
67U TYR 3.5 5.4 - - - +
68U LEU* 3.5 20.6 - - + -
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Residues in contact with ALA 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U PHE* 4.2 5.1 + - + -
31U ALA* 1.3 70.8 - - - +
33U ILE* 1.3 61.2 + - - +
34U TYR* 3.6 28.7 - - + +
40U TYR* 3.8 16.6 - - + -
42U CYS 4.2 0.2 - - - -
66U VAL* 3.6 1.6 - - - -
67U TYR* 2.8 43.7 + - + +
70U ARG* 5.0 7.0 - - + -
141U PHE* 4.3 15.7 - - + -
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Residues in contact with ILE 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U ALA* 4.6 4.3 - - + +
32U ALA* 1.3 75.0 - - - +
34U TYR* 1.3 63.4 + - - +
40U TYR* 3.7 4.3 - - - -
41U VAL* 2.9 26.3 + - + +
42U CYS 3.0 21.3 + - - +
43U GLY 3.9 19.5 - - - +
44U GLY* 4.6 0.2 - - - -
52U VAL* 4.4 11.4 - - + -
54U SER* 4.1 8.5 - - - +
59U PHE* 3.9 32.1 - - + -
64U TYR* 4.1 15.0 - - + -
65U ILE 3.5 7.4 - - - +
66U VAL* 4.0 21.8 - - + -
106U LEU* 3.9 21.1 - - + -
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Residues in contact with TYR 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U ALA* 3.6 28.3 - - + +
33U ILE* 1.3 77.4 - - - +
35U ARG* 1.3 61.1 + - - +
38U VAL* 3.4 26.5 - - + -
39U THR* 3.3 18.4 - - - +
40U TYR* 3.9 14.8 - + + -
41U VAL* 3.8 4.0 - - - -
64U TYR* 3.4 8.2 - - - -
65U ILE* 2.8 38.6 + - + +
67U TYR* 3.7 29.6 - + + -
70U ARG* 3.0 20.2 + - - -
72U ARG 3.8 0.3 + - - -
73U LEU* 2.7 49.8 + - + +
74U ASN* 5.4 3.6 - - - -
141U PHE* 5.1 0.5 - - - -
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Residues in contact with ARG 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U TYR* 1.3 73.4 - - - +
36U ARG* 1.3 71.5 + - - +
37U HIS* 3.1 63.4 + - + +
38U VAL* 3.5 5.9 - - - -
39U THR* 2.9 32.8 + - - +
41U VAL* 3.5 19.2 - - + +
60U TYR* 3.8 43.7 - - - +
63U ASP* 3.2 35.2 + - + +
64U TYR* 3.8 27.4 - - + -
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Residues in contact with ARG 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U TYR 4.2 0.2 + - - -
35U ARG* 1.3 94.0 + - - +
37U HIS* 1.3 64.9 + - - +
38U VAL* 4.6 7.9 - - + -
62U GLU* 3.0 28.1 + - - +
63U ASP* 2.6 30.0 + - - +
64U TYR 3.8 7.1 + - - -
65U ILE* 3.6 36.0 - - + +
82U LYS* 4.7 10.1 - - - +
84U GLU* 3.0 41.4 + - - -
110U LYS* 5.5 1.6 - - - +
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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