Contacts of the strand formed by residues 38 - 48 (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 VAL 38 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34U TYR* 3.4 40.0 - - + -
35U ARG 3.5 12.8 - - - +
36U ARG* 4.6 7.4 - - + -
37U SER* 1.3 88.6 - - + +
39U THR* 1.3 64.1 + - - +
65U ILE* 4.2 22.4 - - + -
67U TYR* 6.4 0.7 - - + -
74U ASN* 5.1 6.6 - - - +
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Residues in contact with THR 39 (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* 3.3 6.3 - - - -
35U ARG* 2.9 33.0 + - - +
37U HIS* 2.8 42.1 - - + +
38U VAL* 1.3 80.0 - - - +
40U TYR* 1.3 67.2 + - - +
41U VAL* 4.0 0.9 - - - +
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Residues in contact with TYR 40 (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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30U PHE* 3.5 15.4 - - - -
32U ALA* 3.8 20.8 - - + -
33U ILE 3.7 7.9 - - - -
34U TYR* 3.9 17.5 - + + -
39U THR* 1.3 78.0 + - - +
41U VAL* 1.3 63.6 + - - +
42U CYS* 3.2 35.4 + - - -
43U GLY* 3.3 10.6 + - - -
73U LEU* 3.5 33.9 - - + -
141U PHE* 3.7 23.0 + + + +
151U TYR* 4.2 31.0 + + + -
193U GLY 3.5 22.6 + - - -
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Residues in contact with VAL 41 (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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33U ILE* 2.9 18.1 + - + +
34U TYR 3.8 3.6 - - - -
35U ARG* 3.5 42.6 - - + +
39U THR* 4.0 1.8 - - - +
40U TYR* 1.3 82.2 - - - +
42U CYS* 1.3 79.9 + - + +
58U CYS* 3.6 27.8 - - + +
59U PHE* 4.8 2.9 - - + -
64U TYR* 4.1 12.6 - - + -
151U TYR* 5.3 1.4 + - - -
193U GLY* 5.0 2.3 - - - +
1247U SO4 3.6 13.7 + - - -
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Residues in contact with CYS 42 (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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33U ILE* 3.0 32.1 + - + +
40U TYR* 3.2 16.2 + - - -
41U VAL* 1.3 94.1 - - + +
43U GLY* 1.3 68.3 + - - +
54U SER* 4.3 2.0 - - - +
58U CYS* 2.0 54.7 - - + -
59U PHE* 5.3 0.7 - - + -
193U GLY 4.8 2.5 - - - -
195U SER* 3.2 19.5 - - - +
1247U SO4 4.3 4.9 - - - -
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Residues in contact with GLY 43 (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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30U PHE* 3.9 11.7 - - - -
31U ALA 3.5 6.5 - - - -
33U ILE* 3.9 3.6 - - - +
40U TYR* 3.3 13.6 + - - -
42U CYS* 1.3 76.3 - - - +
44U GLY* 1.3 57.5 + - - -
54U SER* 2.9 22.9 + - - -
193U GLY 4.8 1.4 + - - -
194U ASP 4.9 1.5 + - - -
195U SER 2.8 13.6 + - - -
196U GLY* 3.3 11.1 - - - -
197U GLY* 4.0 3.8 - - - -
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Residues in contact with GLY 44 (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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30U PHE* 3.6 13.2 - - - -
31U ALA* 2.9 33.2 + - - -
33U ILE* 4.6 0.9 - - - -
43U GLY* 1.3 74.4 - - - -
45U SER* 1.3 66.0 + - - -
52U VAL* 4.1 9.4 - - - -
53U ILE 3.3 12.8 - - - -
54U SER* 4.4 1.1 - - - -
196U GLY 3.6 7.6 + - - -
197U GLY* 4.2 0.2 - - - -
198U PRO* 4.1 1.2 - - - +
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Residues in contact with SER 45 (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* 3.3 8.7 - - - -
31U ALA* 4.9 0.2 - - - -
44U GLY* 1.3 76.2 + - - -
46U LEU* 1.3 62.5 + - - +
47U ILE 3.3 1.6 + - - -
52U VAL* 3.2 6.8 - - - +
53U ILE* 2.8 50.3 + - - +
121U ILE* 4.1 19.1 - - - -
196U GLY 4.9 0.7 + - - -
197U GLY 4.6 0.7 - - - -
198U PRO* 3.1 34.4 - - - +
209U LEU* 4.3 4.5 - - - +
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Residues in contact with LEU 46 (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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28U PRO 5.4 0.4 - - - +
29U TRP* 2.9 17.8 + - - +
31U ALA* 4.9 0.8 - - - +
45U SER* 1.3 69.4 - - - +
47U ILE* 1.3 58.2 + - - +
48U SER 3.3 22.7 - - - +
49U PRO* 4.2 3.1 - - + +
51U TRP 3.6 7.0 - - - +
52U VAL* 3.8 13.2 - - + +
68U LEU* 3.8 28.7 - - + -
108U ILE* 4.0 10.3 - - + -
112U ALA* 4.3 6.7 - - + -
118U ILE* 4.1 24.2 - - + -
119U GLN* 3.8 20.5 - - - +
120U THR* 3.2 16.3 - - + -
121U ILE* 2.9 26.4 + - - +
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Residues in contact with ILE 47 (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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45U SER 3.3 2.0 + - - +
46U LEU* 1.3 76.0 - - - +
48U SER* 1.3 63.4 + - - +
51U TRP* 3.0 23.5 + - + +
53U ILE* 3.8 28.3 - - + +
105U LEU* 4.1 26.2 - - + -
120U THR* 4.0 8.0 - - - -
121U ILE* 3.8 28.4 - - + +
123U LEU* 3.9 30.7 - - + +
209U LEU* 4.1 1.3 - - + -
238U ILE* 4.4 17.5 - - + -
242U THR* 5.0 3.4 - - + -
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Residues in contact with SER 48 (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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46U LEU* 3.3 16.1 - - - +
47U ILE* 1.3 81.1 - - - +
49U PRO* 1.3 77.7 - - - +
50U CYS* 3.1 3.3 + - - +
51U TRP* 3.2 44.6 + - - +
120U THR* 3.6 11.8 - - - +
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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